Chromosome Biomarker

ABSTRACT

A process for analysing chromosome regions and interactions relating to physical performance.

CROSS-REFERENCE

This application is the National Phase application of International Application No. PCT/GB2019/052996, filed Oct. 21, 2019, claiming benefit of United Kingdom Application No. 1817181.9, filed Oct. 22, 2018 and United Kingdom Application No. 1904066.6, filed Mar. 25, 2019. These applications, in their entirety, are incorporated herein by reference.

FIELD OF THE INVENTION

The invention relates to detecting chromosome interactions.

BACKGROUND OF THE INVENTION

Physical performance is complex and cannot be predicted using available methods. It is clear coordination, flexibility, precision, power, speed, endurance, balance, awareness efficiency, and timing are relevant to performance.

SUMMARY OF THE INVENTION

The inventors have identified chromosomal interactions relevant to physical performance using an approach which analyses subgroups in a population. The inventors' work allows physical performance to be typed and modulated in an entirely new way which is more sensitive and personalised than genomic or protein typing, and which reflects the individual history of the individual. This has applications in fitness and physical training regimes, as well as in sports medicine.

Accordingly, the invention provides a process for detecting a chromosome state which represents a subgroup in a population comprising determining whether a chromosome interaction relating to that chromosome state is present or absent within a defined region of the genome, wherein said subgroup relates to physical performance in an individual; and

-   -   wherein said chromosome interaction has optionally been         identified by a method of determining which chromosomal         interactions are relevant to a chromosome state corresponding to         a physical performance subgroup of the population, comprising         contacting a first set of nucleic acids from subgroups with         different states of the chromosome with a second set of index         nucleic acids, and allowing complementary sequences to         hybridise, wherein the nucleic acids in the first and second         sets of nucleic acids represent a ligated product comprising         sequences from both the chromosome regions that have come         together in chromosomal interactions, and wherein the pattern of         hybridisation between the first and second set of nucleic acids         allows a determination of which chromosomal interactions are         specific to a physical performance subgroup; and     -   wherein the chromosome interaction either:

(i) corresponds to any one of the chromosome interactions shown in any of Tables 3, 7, 8, 9, 25 and 30; and/or

(ii) corresponds to any one of the chromosome interactions shown in any of Tables 13, 14, 18, 22, 23 and 24; and/or

(iii) corresponds to any one of the chromosome interactions shown in Table 31 or 32; and/or

(iv) is present in a 4,000 base region which comprises or which flanks (i), (ii) or (iii); and/or

(v) is present in any one of the regions or genes listed in Table 21, 24, 25, 30, 31 or 32.

In a preferred embodiment, the invention provides a process for detecting a chromosome state which represents a subgroup in a population comprising determining whether a chromosome interaction relating to that chromosome state is present or absent within a defined region of the genome, wherein said subgroup relates to physical performance in an individual; and wherein the chromosome interaction either:

(a) corresponds to any one of the chromosome interactions shown in any of Tables 33, 34, 35, 36, 37, 38, 39, 40 or 41, or in any of FIG. 16, 17 or 18; and/or

(b) is present in a 4,000 base region which comprises or which flanks (a).

DETAILED DESCRIPTION OF THE INVENTION Aspects of the Invention

The inventions concerns a panel of epigenetic markers which relate to the regulation and stratification of physical performance, in particular strength and endurance. The markers are preferably stable and may allow detection of a predisposition in physiology to a specific stimulus, such as physical training.

The invention also includes monitoring of physical performance or responsiveness of physical performance to a specific stimulus, such as a specific training regimen. The invention therefore provides in one aspect a ‘live’ ongoing readout of physical performance status allowing a personalised stimulus to be given to the individual which reflects the individual's needs.

The inventions provided a method of selecting an individual for a given physical task, such as racing or specific training. The invention also provides a method of selecting or designing a training or fitness regime, for example for a specific individual.

The invention also provides methods of predicting physical performance, including whether an individual would have high strength or endurance or both, for example as measured in any specific way described herein.

The invention allows categorisation of individuals into ‘fit’, ‘strong’, or ‘sedentary’. The invention allows stratification of ‘baseline’ individuals entering training programmes for better predisposition for either strength, or endurance—de facto predictive biomarkers for response. The invention also allows stratification of early biomarker evidence of response to training in individuals—de facto early response biomarkers for monitoring training progress.

Any marker disclosed herein may be used in the method of the invention, including any marker disclosed in any table or Figure. Preferred markers are shown in:

-   -   Tables 3, 7, 8, 9, 25 and 30; and     -   Tables 13, 14, 18, 22, 23 and 24; and     -   Table 31 or 32; and     -   Tables 33 to 41; and

FIGS. 16 to 18.

Physical Performance

The invention relates to determining physical performance. The process of the invention may detect responsiveness to a stimulus relating to physical performance, for example to training, such as strength or endurance training. The training typically comprises subjecting the individual to physical exertion, for example in terms of the applying force, moving physically, running or carrying out a specific physical activity (for example as disclosed herein) over a certain time period. The process of the invention may be used to detect a high or low response to the stimulus, such as a high or low response to any specific training or physical activity disclosed herein. Preferably the invention detects the response to strength or endurance training.

The invention can be used to select an individual suitable for a physical activity, such as a sport. Preferred sports including strength or endurance sports. A preferred endurance sport is racing or running. Thus the invention may be used to select an individual that is suited to any particular activity mentioned herein, such as training.

The Process of the Invention

The process of the invention comprises a typing system for detecting chromosome interactions relevant to physical performance. This typing may be performed using the EpiSwitch™ system mentioned herein which is based on cross-linking regions of chromosome which have come together in the chromosome interaction, subjecting the chromosomal DNA to cleavage and then ligating the nucleic acids present in the cross-linked entity to derive a ligated nucleic acid with sequence from both the regions which formed the chromosomal interaction. Detection of this ligated nucleic acid allows determination of the presence or absence of a particular chromosome interaction.

The chromosomal interactions may be identified using the above described method in which populations of first and second nucleic acids are used. These nucleic acids can also be generated using EpiSwitch™ technology.

The Epigenetic Interactions Relevant to the Invention

As used herein, the term ‘epigenetic’ and ‘chromosome’ interactions typically refer to interactions between distal regions of a chromosome, said interactions being dynamic and altering, forming or breaking depending upon the status of the region of the chromosome.

In particular processes of the invention chromosome interactions are typically detected by first generating a ligated nucleic acid that comprises sequence from both regions of the chromosomes that are part of the interactions. In such processes the regions can be cross-linked by any suitable means. In a preferred embodiment, the interactions are cross-linked using formaldehyde, but may also be cross-linked by any aldehyde, or D-Biotinoyl-e-aminocaproic acid-N-hydroxysuccinimide ester or Digoxigenin-3-O-methylcarbonyl-e-aminocaproic acid-N-hydroxysuccinimide ester. Para-formaldehyde can cross link DNA chains which are 4 Angstroms apart. Preferably the chromosome interactions are on the same chromosome and optionally 2 to 10 Angstroms apart.

The chromosome interaction may reflect the status of the region of the chromosome, for example, if it is being transcribed or repressed. Chromosome interactions which are specific to subgroups as defined herein have been found to be stable, thus providing a reliable means of measuring the differences between the two subgroups.

In addition, chromosome interactions specific to a characteristic (such as physical performance) will normally occur early in a biological process, for example compared to other epigenetic markers such as methylation or changes to binding of histone proteins, and are also capable of providing a ‘live’ readout of the status of the individual. Thus the process of the invention is able to detect early stages of a biological process as well as allowing continuous monitoring. Chromosome interactions also reflect the current state of the individual and therefore can be used to assess changes to physical performance. Furthermore there is little variation in the relevant chromosome interactions between individuals within the same subgroup. Detecting chromosome interactions is highly informative with up to 50 different possible interactions per gene, and so processes of the invention can interrogate 500,000 different interactions.

Preferred Marker Sets

Herein the term ‘marker’ or ‘biomarker’ refers to a specific chromosome interaction which can be detected (typed) in the invention. Specific markers are disclosed herein, any of which may be used in the invention or any of which may be used in any combination with other specific markers or combinations disclosed herein. Preferably sets of markers may be used, for example in the combinations or numbers disclosed herein. The specific markers disclosed in the tables herein are preferred as well as markers presents in genes and regions mentioned in the tables herein are preferred. These may be typed by any suitable method, for example the PCR or probe based methods disclosed herein, including a qPCR method. The markers are defined herein by location or by probe and/or primer sequences.

Location and Causes of Epigenetic Interactions

Epigenetic chromosomal interactions may overlap and include the regions of chromosomes shown to encode relevant or undescribed genes, but equally may be in intergenic regions. The chromosome interactions which are detected in the invention could be caused by changes to the underlying DNA sequence, by environmental factors, DNA methylation, non-coding antisense RNA transcripts, non-mutagenic carcinogens, histone modifications, chromatin remodelling and specific local DNA interactions. The changes which lead to the chromosome interactions may be caused by changes to the underlying nucleic acid sequence, which themselves do not directly affect a gene product or the mode of gene expression. Such changes may be for example, SNPs within and/or outside of the genes, gene fusions and/or deletions of intergenic DNA, microRNA, and non-coding RNA. For example, it is known that roughly 20% of SNPs are in non-coding regions, and therefore the process as described is also informative in non-coding situation. In one embodiment the regions of the chromosome which come together to form the interaction are less than 5 kb, 3 kb, 1 kb, 500 base pairs or 200 base pairs apart on the same chromosome.

The chromosome interaction which is detected is preferably within any of the genes mentioned in Table 21. However it may also be upstream, for example up to 50,000, up to 30,000, up to 20,000, up to 10,000 or up to 5000 bases upstream from the gene. It may be downstream, for example up to 50,000, up to 30,000, up to 20,000, up to 10,000 or up to 5000 bases downstream from the gene. It may be upstream or downstream from coding sequences, for example by any of these specific numbers of bases.

Subgroups, Time Points and Personalisation

One aim of the present invention is to determine a characteristic relevant to physical performance. This may be at one or more defined time points for the same individual, for example at at least 1, 2, 5, 8 or 10 different time points. The durations between the time points may be at least 20, 50, 80 or 100 days. Typically testing of the individual (by the process of the invention) may occur before a physical stimulus is applied, or during or after. The testing may determine the predisposition to certain types of response, or the actual response to the stimulus.

As used herein, a “subgroup” preferably refers to a population subgroup (a subgroup in a population), more preferably a subgroup in the population of a human or horse population. The invention includes detecting and applying a physical stimulus to particular subgroups in a population. The inventors have discovered that chromosome interactions differ between subsets (for example at least two subsets) in a given population. Identifying these differences will allow categorisation of individuals and this allows personalised stimuli to be given, such a personalised training, or allows selection of the individual for particular physical activities.

Generating Ligated Nucleic Acids

Certain embodiments of the invention utilise ligated nucleic acids, in particular ligated DNA. These comprise sequences from both of the regions that come together in a chromosome interaction and therefore provide information about the interaction. The EpiSwitch™ method described herein uses generation of such ligated nucleic acids to detect chromosome interactions.

Thus a process of the invention may comprise a step of generating ligated nucleic acids (e.g. DNA) by the following steps (including a method comprising these steps):

(i) cross-linking of epigenetic chromosomal interactions present at the chromosomal locus, preferably in vitro;

(ii) optionally isolating the cross-linked DNA from said chromosomal locus;

(iii) subjecting said cross-linked DNA to cutting, for example by restriction digestion with an enzyme that cuts it at least once (in particular an enzyme that cuts at least once within said chromosomal locus);

(iv) ligating said cross-linked cleaved DNA ends (in particular to form DNA loops); and

(v) optionally identifying the presence of said ligated DNA and/or said DNA loops, in particular using techniques such as PCR (polymerase chain reaction), to identify the presence of a specific chromosomal interaction.

These steps may be carried out to detect the chromosome interactions for any embodiment mentioned herein. The steps may also be carried out to generate the first and/or second set of nucleic acids mentioned herein.

PCR (polymerase chain reaction) may be used to detect or identify the ligated nucleic acid, for example the size of the PCR product produced may be indicative of the specific chromosome interaction which is present, and may therefore be used to identify the status of the locus. In preferred embodiments at least 1, 2 or 3 primers or primer pairs as shown in Table 24, 25 or 30 are used in the PCR reaction. In other preferred embodiments at least 1, 2 or 3 primers or primer pairs as shown in Table 31 or 32 are used in the PCR reaction. The skilled person will be aware of numerous restriction enzymes which can be used to cut the DNA within the chromosomal locus of interest. It will be apparent that the particular enzyme used will depend upon the locus studied and the sequence of the DNA located therein. A non-limiting example of a restriction enzyme which can be used to cut the DNA as described in the present invention is Taql.

Embodiments Such as EpiSwitch™ Technology

The EpiSwitch™ Technology also relates to the use of microarray EpiSwitch™ marker data in the detection of epigenetic chromosome conformation signatures specific for phenotypes. Embodiments such as EpiSwitch™ which utilise ligated nucleic acids in the manner described herein have several advantages. They have a low level of stochastic noise, for example because the nucleic acid sequences from the first set of nucleic acids of the present invention either hybridise or fail to hybridise with the second set of nucleic acids. This provides a binary result permitting a relatively simple way to measure a complex mechanism at the epigenetic level. EpiSwitch™ technology also has fast processing time and low cost. In one embodiment the processing time is 3 hours to 6 hours.

Samples and Sample Treatment

The process of the invention will normally be carried out on a sample. The sample may be obtained at a defined time point, for example at any time point defined herein. The sample will normally contain DNA from the individual. It will normally contain cells. In one embodiment a sample is obtained by minimally invasive means and may for example be a blood sample. DNA may be extracted and cut up with a standard restriction enzyme. This can pre-determine which chromosome conformations are retained and will be detected with the EpiSwitch™ platforms. Due to the synchronisation of chromosome interactions between tissues and blood, including horizontal transfer, a blood sample can be used to detect the chromosome interactions in tissues.

Properties of Nucleic Acids of the Invention

The invention relates to certain nucleic acids, such as the ligated nucleic acids which are described herein as being used or generated in the process of the invention. These may be the same as, or have any of the properties of, the first and second nucleic acids mentioned herein. The nucleic acids of the invention typically comprise two portions each comprising sequence from one of the two regions of the chromosome which come together in the chromosome interaction. Typically each portion is at least 8, 10, 15, 20, 30 or 40 nucleotides in length, for example 10 to 40 nucleotides in length. Preferred nucleic acids comprise sequence from any of the genes mentioned in any of the tables, including Table 21. Typically preferred nucleic acids comprise the specific probe sequences mentioned in Table 24, 25 or 30; or fragments and/or homologues of such sequences. Preferred nucleic acids also comprise the specific probe sequences mentioned in Table 31 or 32; or fragments and/or homologues of such sequences. Preferably the nucleic acids are DNA. It is understood that where a specific sequence is provided the invention may use the complementary sequence as required in the particular embodiment.

The primers shown in Table 24, 25 or 30 may also be used in the invention as mentioned herein. In one embodiment primers are used which comprise any of: the sequences shown in Table 24, 25 or 30; or fragments and/or homologues of any sequence shown in Table 24, 25 or 30.

The primers shown in Table 31 or 32 may also be used in the invention as mentioned herein. In one embodiment primers are used which comprise any of: the sequences shown in Table 31 or 32; or fragments and/or homologues of any sequence shown in Table 31 or 32.

The Second Set of Nucleic Acids—the ‘Index’ Sequences

The second set of nucleic acid sequences has the function of being a set of index sequences, and is essentially a set of nucleic acid sequences which are suitable for identifying subgroup specific sequence. They can represents the ‘background’ chromosomal interactions and might be selected in some way or be unselected. They are in general a subset of all possible chromosomal interactions.

The second set of nucleic acids may be derived by any suitable process. They can be derived computationally or they may be based on chromosome interaction in individuals. They typically represent a larger population group than the first set of nucleic acids. In one particular embodiment, the second set of nucleic acids represents all possible epigenetic chromosomal interactions in a specific set of genes. In another particular embodiment, the second set of nucleic acids represents a large proportion of all possible epigenetic chromosomal interactions present in a population described herein. In one particular embodiment, the second set of nucleic acids represents at least 50% or at least 80% of epigenetic chromosomal interactions in at least 20, 50, 100 or 500 genes, for example in 20 to 100 or 50 to 500 genes.

The second set of nucleic acids typically represents at least 100 possible epigenetic chromosome interactions which modify, regulate or in any way mediate a phenotype in population. The second set of nucleic acids may represent chromosome interactions that affect a physical characteristic. The second set of nucleic acids typically comprises sequences representing epigenetic interactions both relevant and not relevant to a physical performance subgroup.

In one particular embodiment the second set of nucleic acids derive at least partially from naturally occurring sequences in a population, and are typically obtained by in silico processes. Said nucleic acids may further comprise single or multiple mutations in comparison to a corresponding portion of nucleic acids present in the naturally occurring nucleic acids. Mutations include deletions, substitutions and/or additions of one or more nucleotide base pairs. In one particular embodiment, the second set of nucleic acids may comprise sequence representing a homologue and/or orthologue with at least 70% sequence identity to the corresponding portion of nucleic acids present in the naturally occurring species. In another particular embodiment, at least 80% sequence identity or at least 90% sequence identity to the corresponding portion of nucleic acids present in the naturally occurring species is provided.

Properties of the Second Set of Nucleic Acids

In one particular embodiment, there are at least 100 different nucleic acid sequences in the second set of nucleic acids, preferably at least 1000, 2000 or 5000 different nucleic acids sequences, with up to 100,000, 1,000,000 or 10,000,000 different nucleic acid sequences. A typical number would be 100 to 1,000,000, such as 1,000 to 100,000 different nucleic acids sequences. All or at least 90% or at least 50% or these would correspond to different chromosomal interactions.

In one particular embodiment, the second set of nucleic acids represent chromosome interactions in at least 20 different loci or genes, preferably at least 40 different loci or genes, and more preferably at least 100, at least 500, at least 1000 or at least 5000 different loci or genes, such as 100 to 10,000 different loci or genes. The lengths of the second set of nucleic acids are suitable for them to specifically hybridise according to Watson Crick base pairing to the first set of nucleic acids to allow identification of chromosome interactions specific to subgroups. Typically the second set of nucleic acids will comprise two portions corresponding in sequence to the two chromosome regions which come together in the chromosome interaction. The second set of nucleic acids typically comprise nucleic acid sequences which are at least 10, preferably 20, and preferably still 30 bases (nucleotides) in length. In another embodiment, the nucleic acid sequences may be at the most 500, preferably at most 100, and preferably still at most 50 base pairs in length. In a preferred embodiment, the second set of nucleic acids comprises nucleic acid sequences of between 17 and 25 base pairs. In one embodiment at least 100, 80% or 50% of the second set of nucleic acid sequences have lengths as described above. Preferably the different nucleic acids do not have any overlapping sequences, for example at least 100%, 90%, 80% or 50% of the nucleic acids do not have the same sequence over at least 5 contiguous nucleotides.

Given that the second set of nucleic acids acts as an ‘index’ then the same set of second nucleic acids may be used with different sets of first nucleic acids which represent subgroups for different characteristics, i.e. the second set of nucleic acids may represent a ‘universal’ collection of nucleic acids which can be used to identify chromosome interactions relevant to different characteristics.

The First Set of Nucleic Acids

The first set of nucleic acids are typically from subgroups relevant to physical performance. The first nucleic acids may have any of the characteristics and properties of the second set of nucleic acids mentioned herein. The first set of nucleic acids is normally derived from samples from the individuals which have undergone treatment and processing as described herein, particularly the EpiSwitch™ cross-linking and cleaving steps. Typically the first set of nucleic acids represents all or at least 80% or 50% of the chromosome interactions present in the samples taken from the individuals.

Typically, the first set of nucleic acids represents a smaller population of chromosome interactions across the loci or genes represented by the second set of nucleic acids in comparison to the chromosome interactions represented by second set of nucleic acids, i.e. the second set of nucleic acids is representing a background or index set of interactions in a defined set of loci or genes.

Library of Nucleic Acids

Any of the types of nucleic acid populations mentioned herein may be present in the form of a library comprising at least 200, at least 500, at least 1000, at least 5000 or at least 10000 different nucleic acids of that type, such as ‘first’ or ‘second’ nucleic acids. Such a library may be in the form of being bound to an array. A library may for example comprise all of the nucleic acids disclosed in any table disclosed herein, or all of the probe sequences disclosed in any table herein.

Hybridisation

The invention requires a means for allowing wholly or partially complementary nucleic acid sequences from the first set of nucleic acids and the second set of nucleic acids to hybridise. In one embodiment all of the first set of nucleic acids is contacted with all of the second set of nucleic acids in a single assay, i.e. in a single hybridisation step. However any suitable assay can be used.

Labelled Nucleic Acids and Pattern of Hybridisation

The nucleic acids mentioned herein may be labelled, preferably using an independent label such as a fluorophore (fluorescent molecule) or radioactive label which assists detection of successful hybridisation. Certain labels can be detected under UV light. The pattern of hybridisation, for example on an array described herein, represents differences in epigenetic chromosome interactions between the two subgroups, and thus provides a process of comparing epigenetic chromosome interactions and determination of which epigenetic chromosome interactions are specific to a subgroup in the population of the present invention.

The term ‘pattern of hybridisation’ broadly covers the presence and absence of hybridisation between the first and second set of nucleic acids, i.e. which specific nucleic acids from the first set hybridise to which specific nucleic acids from the second set, and so it not limited to any particular assay or technique, or the need to have a surface or array on which a ‘pattern’ can be detected.

Selecting a Subgroup with Particular Characteristics

The invention provides a process which comprises detecting the presence or absence of chromosome interactions, typically 5 to 20 or 5 to 500 such interactions, preferably 20 to 300 or 50 to 100 interactions, in order to determine the presence or absence of a characteristic relating to physical performance in an individual. Preferably the chromosome interactions are those in any of the genes mentioned herein or in any Table herein. In one embodiment the chromosome interactions which are typed are those represented in any of Tables 3, 7, 8, 9, 25 and 30. In another embodiment the chromosome interactions are those represented in any of Tables 13, 14, 18, 22, 23 and 24. In a preferred embodiment the chromosome interactions which are typed are those represented in Table 31 or 32. In one embodiment the chromosome interactions which are typed are those from any of Tables 33, 34, 35, 36, 37, 38, 39 or 40 or in any of FIG. 16, 17 or 18. The relevant chromosome interaction may be present or absent for a given characteristic, and therefore either presence or absence of the interaction will indicate the presence of the characteristic.

The Individual that is Tested

The individual that is tested is preferably a human or horse. The human be an athlete or sportsman. The human is typically 30 years old or less. The horse may be any type of horse mentioned herein, such as a Thoroughbred. The horse may be racing horse. The horse may be one which is not a racing horse, but which optionally is being considered for selection as a race horse. The horse may be less than 500 days old, such as less than 200 or less than 100 days old.

Preferred Gene Regions, Loci, Genes and Chromosome Interactions

For all aspects of the invention preferred gene regions, loci, genes and chromosome interactions are mentioned in the tables, for example in any of Tables 3, 7, 8, 9, 25 and 30 (preferably for typing humans) or in any of Tables 13, 14, 18, 22, 23 and 24 (preferably for typing horses), or in Table 31 or 32 (preferably for typing humans). Typically in the processes of the invention chromosome interactions are detected from at least 1, 2, 10, 30 or 50 genes listed in Table 21. The chromosome interaction may be upstream or downstream of any of the genes mentioned herein, for example 50 kb upstream or 20 kb downstream, for example from the coding sequence.

In one embodiment at least 5, 10 or all of the chromosome interactions of Table 3 are typed. In one embodiment at least the interactions with the top 5 or 10 highest odds ratio of Table 3 are typed.

In one embodiment at least 5, 10, 15 or all of the chromosome interactions in Table 7 are typed. In one embodiment at least the interactions with the smallest 5, 10 or 15 mean p values of Table 7 are typed.

In one embodiment at least 5, 10, 15, 20 or all of the chromosome interactions in Table 8 are typed. In one embodiment at least the interactions with the smallest 5, 10, 15 or 20 mean p values of Table 8 are typed.

In one embodiment at least 5, 10, 15, 20 or all of the chromosome interactions in Table 9 are typed. In one embodiment at least the interactions with the smallest 5, 10, 15 or 20 mean p values of Table 9 are typed.

In one embodiment at least 5, 10, 15 or all of the chromosome interactions in Table 13 are typed. In one embodiment at least the interactions with the smallest 5 or 10 Exact Boschloo p value of Table 13 are typed.

In one embodiment at least 5, 10, 15 or all of the chromosome interactions in Table 14 are typed.

In one embodiment at least 5, 10, 20, 30 or all of the chromosome interactions in Table 18 are typed. In one embodiment at least the interactions with the smallest 5, 10, 20 or 30 Exact Boschloo p value of Table 18 are typed.

In one embodiment at least 5, 10 or all of the chromosome interactions of Table 22 are typed. In one embodiment at least the interactions with the top 5 or 10 highest odds ratio of Table 22 are typed.

In one embodiment at least 5, 10, 15 or all of the chromosome interactions of Table 23 are typed.

In one embodiment at least 5, 10, 20, 30 or all of the chromosome interactions of Table 24 are typed. In one embodiment at least the interactions with the top 5, 10, 20, 30 GLMNET values of Table 24 are typed.

In one embodiment at least 5, 10, 20, 30, 40, 50 or all of the chromosome interactions of Table 25 are typed. In one embodiment at least the interactions with the smallest 5, 10, 20, 30, 40, 50 adjusted p values of Table 25 are typed. In one embodiment at least the markers numbered 1 to 30 in Table 25 are typed. In another at least the markers numbers 31 to 77 in Table 25 are typed.

In one embodiment at least 5, 10, 20, 30, 40, 50, 150, 180 or all of the chromosome interactions of Table 30 are typed. In one embodiment at least the interactions with the smallest 5, 10, 20, 30, 40, 50, 150, or 180 adjusted p values of Table 30 are typed. In one embodiment at least the markers numbered 1 to 50 in Table 30 are typed. In another embodiment at least the markers numbered 51 to 100 in Table 30 are typed. In another embodiment at least the markers numbered 101 to 150 in Table 30 are typed. In one embodiment at least the markers numbered 151 to 202 in Table 30 are typed.

In one embodiment at least 5, 10 or all of the chromosome interactions of Table 31 are typed.

In one embodiment at least 5 or all of the chromosome interactions of Table 32 are typed.

In one embodiment at least 5, 10, 20, 30, 40, 50, 150, 180, 200, 250 or all of the chromosome interactions of Table 33 are typed. In one embodiment at least the interactions with the smallest 5, 10, 20, 30, 40, 50, 150, 180 or 250 adjusted p values of Table 33 are typed. In one embodiment at least the markers numbered 1 to 50 in Table 33 are typed. In another embodiment at least the markers numbered 51 to 100 in Table 33 are typed. In another embodiment at least the markers numbered 101 to 150 in Table 33 are typed. In one embodiment at least the markers numbered 151 to 202 in Table 33 are typed. In one embodiment at least the markers numbered 202 to 320 in Table 33 are typed.

In one embodiment at least 5, 10, 20, 30, 40, 50 or all of the chromosome interactions of Table 34 are typed.

In one embodiment at least 5, 10, 20, 30 or all of the chromosome interactions of Table 35 are typed.

In one embodiment at least 5, 10, 15 or all of the chromosome interactions of Table 36 are typed.

In one embodiment at least 5, 10, 20, 30, 40, 50, 150, 180 or all of the chromosome interactions of Table 37 are typed. In one embodiment at least the interactions with the smallest 5, 10, 20, 30, 40, 50, 150, or 180 adjusted p values of Table 37 are typed. In one embodiment at least the markers numbered 1 to 50 in Table 37 are typed. In another embodiment at least the markers numbered 51 to 100 in Table 37 are typed. In another embodiment at least the markers numbered 101 to 150 in Table 37 are typed. In one embodiment at least the markers numbered 151 to 202 in Table 37 are typed.

In one embodiment at least 5, 10 or all of the chromosome interactions of Table 38 are typed.

In one embodiment at least 5 or all of the chromosome interactions of Table 39 are typed.

In one embodiment at least 5, 10 or all of the chromosome interactions of Table 40 are typed. In one embodiment at least the 3 ‘shared’ chromosome interactions of Table 40 are typed. In one embodiment at least the 7 ‘strength’ chromosome interactions of Table 40 are typed.

In one embodiment at least 5, 10, 20, 30, 40, 50 or all of the chromosome interactions of Table 41 are typed. In one embodiment at least the interactions with the smallest 5, 10, 20, 30, 40, 50 adjusted p values of Table 41 are typed. In one embodiment at least the markers numbered 1 to 30 in Table 41 are typed.

In another at least the markers numbers 31 to 77 in Table 41 are typed. [Table 41 is shown in abbreviated form to avoid duplicating information from Table 25 which relates to the same marker set. It is understood that smallest p values mentioned here can be obtained from Table 25]

In one embodiment at least 5, 8 or all of the chromosome interactions of FIG. 16 are typed.

In one embodiment at least 5, 10 or all of the chromosome interactions of FIG. 17 are typed.

In one embodiment at least 5, 8 or all of the chromosome interactions of FIG. 18 are typed.

Typically at least 5, 10, 15, 20, 30, 40 or 70 chromosome interactions are typed from any of genes or regions disclosed the tables herein, or parts of tables disclosed herein. Typically the chromosome interactions which are typed are present in at least 20, 50 or all of the genes mentioned in Table 21.

For all aspects of the invention preferred gene regions, loci, genes and chromosome interactions are mentioned in Tables 24 and 30.

In one embodiment the locus (including the gene and/or place where the chromosome interaction is detected) may comprise a CTCF binding site. This is any sequence capable of binding transcription repressor CTCF. That sequence may consist of or comprise the sequence CCCTC which may be present in 1, 2 or 3 copies at the locus. The CTCF binding site sequence may comprise the sequence CCGCGNGGNGGCAG (in IUPAC notation). The CTCF binding site may be within at least 100, 500, 1000 or 4000 bases of the chromosome interaction or within any of the chromosome regions shown Table 24 or 30.

Thus typically sequence from both regions of the probe (i.e. from both sites of the chromosome interaction) could be detected. In preferred embodiments probes are used in the process which comprise or consist of the same or complementary sequence to a probe shown in any table. In some embodiments probes are used which comprise sequence which is homologous to any of the probe sequences shown in the tables.

Tables Provided Herein

The tables show probe (Episwitch™ marker) data and gene data representing chromosome interactions relevant to physical performance. The probe sequences show sequence which can be used to detect a ligated product generated from both sites of gene regions that have come together in chromosome interactions, i.e. the probe will comprise sequence which is complementary to sequence in the ligated product. The first two sets of Start-End positions show probe positions, and the second two sets of Start-End positions show the relevant 4 kb region. The following information is provided in the probe data table:

-   -   HyperG_Stats: p-value for the probability of finding that number         of significant EpiSwitch™ markers in the locus based on the         parameters of hypergeometric enrichment     -   Probe Count Total: Total number of EpiSwitch™ Conformations         tested at the locus     -   Probe Count Sig: Number of EpiSwitch™ Conformations found to be         statistically significant at the locus     -   FDR HyperG: Multi-test (Fimmunoresposivenesse Discovery Rate)         corrected hypergeometric p-value     -   Percent Sig: Percentage of significant EpiSwitch™ markers         relative the number of markers tested at the locus     -   logFC: logarithm base 2 of Epigenetic Ratio (FC)     -   AveExpr: average log 2-expression for the probe over all arrays         and channels     -   T: moderated t-statistic     -   p-value: raw p-value     -   adj. p-value: adjusted p-value or q-value     -   B—B-statistic (lods or B) is the log-odds that that gene is         differentially expressed.     -   FC—non-log Fold Change     -   FC_1—non-log Fold Change centred around zero     -   LS—Binary value this relates to FC_1 values. FC_1 value below         −1.1 it is set to −1 and if the FC_1 value is above 1.1 it is         set to 1. Between those values the value is 0

The tables also shows genes where a relevant chromosome interaction has been found to occur. The p-value in the loci table is the same as the HyperG_Stats (p-value for the probability of finding that number of significant EpiSwitch™ markers in the locus based on the parameters of hypergeometric enrichment).

The probes are designed to be 30 bp away from the Taq1 site. In case of PCR, PCR primers are typically designed to detect ligated product but their locations from the Taq1 site vary.

Probe Locations:

Start 1-30 bases upstream of Taql site on fragment 1

End 1—Taql restriction site on fragment 1

Start 2—Taql restriction site on fragment 2

End 2-30 bases downstream of Taql site on fragment 2

4 kb Sequence Location:

Start 1-4000 bases upstream of Taql site on fragment 1

End 1—Taql restriction site on fragment 1

Start 2—Taql restriction site on fragment 2

End 2-4000 bases downstream of Taql site on fragment 2

GLMNET values related to procedures for fitting the entire lasso or elastic-net regularization (Lambda set to 0.5 (elastic-net)).

Preferred Embodiments for Sample Preparation and Chromosome Interaction Detection

Methods of preparing samples and detecting chromosome conformations are described herein. Optimised (non-conventional) versions of these methods can be used, for example as described in this section.

Typically the sample will contain at least 2×10⁵ cells. The sample may contain up to 5×10⁵ cells. In one embodiment, the sample will contain 2×10⁵ to 5.5×10⁵ cells

Crosslinking of epigenetic chromosomal interactions present at the chromosomal locus is described herein. This may be performed before cell lysis takes place. Cell lysis may be performed for 3 to 7 minutes, such as 4 to 6 or about 5 minutes. In some embodiments, cell lysis is performed for at least 5 minutes and for less than 10 minutes.

Digesting DNA with a restriction enzyme is described herein. Typically, DNA restriction is performed at about 55° C. to about 70° C., such as for about 65° C., for a period of about 10 to 30 minutes, such as about 20 minutes.

Preferably a frequent cutter restriction enzyme is used which results in fragments of ligated DNA with an average fragment size up to 4000 base pair. Optionally the restriction enzyme results in fragments of ligated DNA have an average fragment size of about 200 to 300 base pairs, such as about 256 base pairs. In one embodiment, the typical fragment size is from 200 base pairs to 4,000 base pairs, such as 400 to 2,000 or 500 to 1,000 base pairs.

In one embodiment of the EpiSwitch method a DNA precipitation step is not performed between the DNA restriction digest step and the DNA ligation step.

DNA ligation is described herein. Typically the DNA ligation is performed for 5 to 30 minutes, such as about 10 minutes.

The protein in the sample may be digested enzymatically, for example using a proteinase, optionally Proteinase K. The protein may be enzymatically digested for a period of about 30 minutes to 1 hour, for example for about 45 minutes. In one embodiment after digestion of the protein, for example Proteinase K digestion, there is no cross-link reversal or phenol DNA extraction step.

In one embodiment PCR detection is capable of detecting a single copy of the ligated nucleic acid, preferably with a binary read-out for presence/absence of the ligated nucleic acid.

FIG. 14 shows a preferred method of detecting chromosome interactions.

Processes and Uses of the Invention

The process of the invention can be described in different ways. It can be described as a method of making a ligated nucleic acid comprising (i) in vitro cross-linking of chromosome regions which have come together in a chromosome interaction; (ii) subjecting said cross-linked DNA to cutting or restriction digestion cleavage; and (iii) ligating said cross-linked cleaved DNA ends to form a ligated nucleic acid, wherein detection of the ligated nucleic acid may be used to determine the chromosome state at a locus, and wherein preferably:

-   -   the locus may be any of the loci, regions or genes mentioned in         any table, and/or     -   wherein the chromosomal interaction may be any of the chromosome         interactions mentioned herein or corresponding to any of the         probes disclosed in any table, and/or     -   wherein the ligated product may have or comprise (i) sequence         which is the same as or homologous to any of the probe sequences         disclosed in any table herein; or (ii) sequence which is         complementary to (ii).

The process of the invention can be described as a process for detecting chromosome states which represent different subgroups in a population comprising determining whether a chromosome interaction is present or absent within a defined epigenetically active region of the genome, wherein preferably:

-   -   the subgroup is defined by presence or absence of physical         performance, and/or     -   the chromosome state may be at any locus, region or gene         mentioned in any table; and/or     -   the chromosome interaction may be any of those mentioned in any         table or corresponding to any of the probes disclosed in that         table.

The process of the invention can be described as a method of making a ligated nucleic acid comprising (i) in vitro cross-linking of chromosome regions which have come together in a chromosome interaction; (ii) subjecting said cross-linked DNA to cutting or restriction digestion cleavage; and (iii) ligating said cross-linked cleaved DNA ends to form a ligated nucleic acid, wherein detection of the ligated nucleic acid may be used to determine the chromosome state at a locus, and wherein preferably:

-   -   the locus may be any of the loci, regions or genes mentioned in         any table, and/or     -   wherein the chromosomal interaction may be any of the chromosome         interactions mentioned herein or corresponding to any of the         probes disclosed in any table, and/or     -   wherein the ligated product may have or comprise (i) sequence         which is the same as or homologous to any of the probe sequences         disclosed in any table; or (ii) sequence which is complementary         to (ii).

The process of the invention can be described as a process for detecting chromosome states which represent different subgroups in a population comprising determining whether a chromosome interaction is present or absent within a defined epigenetically active region of the genome, wherein preferably:

-   -   the subgroup is defined by presence or absence of physical         performance, and/or     -   the chromosome state may be at any locus, region or gene         mentioned in any table; and/or     -   the chromosome interaction may be any of those mentioned in any         table or corresponding to any of the probes disclosed in that         table.

The invention includes detecting chromosome interactions at any locus, gene or regions mentioned in any table, such as Table 24 or 30. The invention includes use of the nucleic acids and probes mentioned herein to detect chromosome interactions, for example use of at least 1, 5, 10, 50, 100 such nucleic acids or probes to detect chromosome interactions, preferably in at least 1, 5, 10, 50, 100 different loci or genes.

The invention includes detection of chromosome interactions using any of the primers or primer pairs listed in Table 24 or 30 or using variants of these primers as described herein (sequences comprising the primer sequences or comprising fragments and/or homologues of the primer sequences).

The invention includes detecting chromosome interactions at any locus, gene or regions mentioned Table 24 or 30. The invention includes use of the nucleic acids and probes mentioned herein to detect chromosome interactions, for example use of at least 1, 5, 10, 50, 100, 200, 250, 300 such nucleic acids or probes to detect chromosome interactions, preferably in at least 1, 5, 10, 50, 100, 200, 250, 300 different loci or genes. The invention includes detection of chromosome interactions using any of the primers or primer pairs listed in Table 24 or 30 or using variants of these primers as described herein (sequences comprising the primer sequences or comprising fragments and/or homologues of the primer sequences).

When analysing whether a chromosome interaction occurs ‘within’ a defined gene, region or location, either both the parts of the chromosome which have together in the interaction are within the defined gene, region or location or in some embodiments only one part of the chromosome is within the defined, gene, region or location.

Use of the Method of the Invention to Identify New Training or Fitness Regimens

Knowledge of chromosome interactions can be used to identify new fitness or training regimens. The invention provides methods and uses of chromosomes interactions defined herein to identify or design new agents.

Homologues

Homologues of polynucleotide/nucleic acid (e.g. DNA) sequences are referred to herein. Such homologues typically have at least 70% homology, preferably at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, at least 98% or at least 99% homology, for example over a region of at least 10, 15, 20, 30, 100 or more contiguous nucleotides, or across the portion of the nucleic acid which is from the region of the chromosome involved in the chromosome interaction. The homology may be calculated on the basis of nucleotide identity (sometimes referred to as “hard homology”).

Therefore, in a particular embodiment, homologues of polynucleotide/nucleic acid (e.g. DNA) sequences are referred to herein by reference to percentage sequence identity. Typically such homologues have at least 70% sequence identity, preferably at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, at least 98% or at least 99% sequence identity, for example over a region of at least 10, 15, 20, 30, 100 or more contiguous nucleotides, or across the portion of the nucleic acid which is from the region of the chromosome involved in the chromosome interaction.

For example the UWGCG Package provides the BESTFIT program which can be used to calculate homology and/or % sequence identity (for example used on its default settings) (Devereux et al (1984) Nucleic Acids Research 12, p 387-395). The PILEUP and BLAST algorithms can be used to calculate homology and/or % sequence identity and/or line up sequences (such as identifying equivalent or corresponding sequences (typically on their default settings)), for example as described in Altschul S. F. (1993) J Mol Evol 36:290-300; Altschul, S, F et al (1990) J Mol Biol 215:403-10.

Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information. This algorithm involves first identifying high scoring sequence pair (HSPs) by identifying short words of length W in the query sequence that either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighbourhood word score threshold (Altschul et al, supra). These initial neighbourhood word hits act as seeds for initiating searches to find HSPs containing them. The word hits are extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Extensions for the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W5 T and X determine the sensitivity and speed of the alignment. The BLAST program uses as defaults a word length (W) of 11, the BLOSUM62 scoring matrix (see Henikoff and Henikoff (1992) Proc. Natl. Acad. Sci. USA 89: 10915-10919) alignments (B) of 50, expectation (E) of 10, M=5, N=4, and a comparison of both strands.

The BLAST algorithm performs a statistical analysis of the similarity between two sequences; see e.g., Karlin and Altschul (1993) Proc. Natl. Acad. Sci. USA 90: 5873-5787. One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two polynucleotide sequences would occur by chance. For example, a sequence is considered similar to another sequence if the smallest sum probability in comparison of the first sequence to the second sequence is less than about 1, preferably less than about 0.1, more preferably less than about 0.01, and most preferably less than about 0.001.

The homologous sequence typically differs by 1, 2, 3, 4 or more bases, such as less than 10, 15 or 20 bases (which may be substitutions, deletions or insertions of nucleotides). These changes may be measured across any of the regions mentioned above in relation to calculating homology and/or % sequence identity.

Homology of a ‘pair of primers’ can be calculated, for example, by considering the two sequences as a single sequence (as if the two sequences are joined together) for the purpose of then comparing against the another primer pair which again is considered as a single sequence.

Arrays

The second set of nucleic acids may be bound to an array, and in one embodiment there are at least 15,000, 45,000, 100,000 or 250,000 different second nucleic acids bound to the array, which preferably represent at least 300, 900, 2000 or 5000 loci. In one embodiment one, or more, or all of the different populations of second nucleic acids are bound to more than one distinct region of the array, in effect repeated on the array allowing for error detection. The array may be based on an Agilent SurePrint G3 Custom CGH microarray platform. Detection of binding of first nucleic acids to the array may be performed by a dual colour system.

Forms of the Substance Mentioned Herein

Any of the substances, such as nucleic acids or therapeutic agents, mentioned herein may be in purified or isolated form. They may be in a form which is different from that found in nature, for example they may be present in combination with other substance with which they do not occur in nature. The nucleic acids (including portions of sequences defined herein) may have sequences which are different to those found in nature, for example having at least 1, 2, 3, 4 or more nucleotide changes in the sequence as described in the section on homology. The nucleic acids may have heterologous sequence at the 5′ or 3′ end. The nucleic acids may be chemically different from those found in nature, for example they may be modified in some way, but preferably are still capable of Watson-Crick base pairing. Where appropriate the nucleic acids will be provided in double stranded or single stranded form. The invention provides all of the specific nucleic acid sequences mentioned herein in single or double stranded form, and thus includes the complementary strand to any sequence which is disclosed.

The invention provides a kit for carrying out any process of the invention, including detection of a chromosomal interaction relating to physical performance. Such a kit can include a specific binding agent capable of detecting the relevant chromosomal interaction, such as agents capable of detecting a ligated nucleic acid generated by processes of the invention. Preferred agents present in the kit include probes capable of hybridising to the ligated nucleic acid or primer pairs, for example as described herein, capable of amplifying the ligated nucleic acid in a PCR reaction.

The invention provides a device that is capable of detecting the relevant chromosome interactions. The device preferably comprises any specific binding agents, probe or primer pair capable of detecting the chromosome interaction, such as any such agent, probe or primer pair described herein.

Detection Methods

In one embodiment quantitative detection of the ligated sequence which is relevant to a chromosome interaction is carried out using a probe which is detectable upon activation during a PCR reaction, wherein said ligated sequence comprises sequences from two chromosome regions that come together in an epigenetic chromosome interaction, wherein said method comprises contacting the ligated sequence with the probe during a PCR reaction, and detecting the extent of activation of the probe, and wherein said probe binds the ligation site. The method typically allows particular interactions to be detected in a MIQE compliant manner using a dual labelled fluorescent hydrolysis probe.

The probe is generally labelled with a detectable label which has an inactive and active state, so that it is only detected when activated. The extent of activation will be related to the extent of template (ligation product) present in the PCR reaction. Detection may be carried out during all or some of the PCR, for example for at least 50% or 80% of the cycles of the PCR.

The probe can comprise a fluorophore covalently attached to one end of the oligonucleotide, and a quencher attached to the other end of the nucleotide, so that the fluorescence of the fluorophore is quenched by the quencher. In one embodiment the fluorophore is attached to the 5′end of the oligonucleotide, and the quencher is covalently attached to the 3′ end of the oligonucleotide. Fluorophores that can be used in the methods of the invention include FAM, TET, JOE, Yakima Yellow, HEX, Cyanine3, ATTO 550, TAMRA, ROX, Texas Red, Cyanine 3.5, LC610, LC 640, ATTO 647N, Cyanine 5, Cyanine 5.5 and ATTO 680. Quenchers that can be used with the appropriate fluorophore include TAM, BHQ1, DAB, Eclip, BHQ2 and BBQ650, optionally wherein said fluorophore is selected from HEX, Texas Red and FAM. Preferred combinations of fluorophore and quencher include FAM with BHQ1 and Texas Red with BHQ2.

Use of the Probe in a GPCR Assay

Hydrolysis probes of the invention are typically temperature gradient optimised with concentration matched negative controls. Preferably single-step PCR reactions are optimized. More preferably a standard curve is calculated. An advantage of using a specific probe that binds across the junction of the ligated sequence is that specificity for the ligated sequence can be achieved without using a nested PCR approach. The methods described herein allow accurate and precise quantification of low copy number targets. The target ligated sequence can be purified, for example gel-purified, prior to temperature gradient optimization. The target ligated sequence can be sequenced. Preferably PCR reactions are performed using about 10 ng, or 5 to 15 ng, or 10 to 20 ng, or 10 to 50 ng, or 10 to 200 ng template DNA.

Forward and reverse primers are designed such that one primer binds to the sequence of one of the chromosome regions represented in the ligated DNA sequence, and the other primer binds to other chromosome region represented in the ligated DNA sequence, for example, by being complementary to the sequence.

Choice of Ligated DNA Target

The invention includes selecting primers and a probe for use in a PCR method as defined herein comprising selecting primers based on their ability to bind and amplify the ligated sequence and selecting the probe sequence based properties of the target sequence to which it will bind, in particular the curvature of the target sequence.

Probes are typically designed/chosen to bind to ligated sequences which are juxtaposed restriction fragments spanning the restriction site. In one embodiment of the invention, the predicted curvature of possible ligated sequences relevant to a particular chromosome interaction is calculated, for example using a specific algorithm referenced herein. The curvature can be expressed as degrees per helical turn, e.g. 10.5° per helical turn. Ligated sequences are selected for targeting where the ligated sequence has a curvature propensity peak score of at least 5° per helical turn, typically at least 100, 15° or 20° per helical turn, for example 5° to 20° per helical turn. Preferably the curvature propensity score per helical turn is calculated for at least 20, 50, 100, 200 or 400 bases, such as for 20 to 400 bases upstream and/or downstream of the ligation site. Thus in one embodiment the target sequence in the ligated product has any of these levels of curvature. Target sequences can also be chosen based on lowest thermodynamic structure free energy.

Particular Embodiments

In one embodiment only intrachromosomal interactions are typed/detected, and no extrachromosomal interactions (between different chromosomes) are typed/detected.

In particular embodiments certain chromosome interactions are not typed, for example any specific interaction mentioned herein (for example as defined by any probe or primer pair mentioned herein). In some embodiments chromosome interactions are not typed in any of the genes mentioned here, for example in any gene mentioned in Table 21.

Publications

The contents of all publications mentioned herein are incorporated by reference into the present specification and may be used to further define the features relevant to the invention.

Tables

Table 1 shows patient sample for the human study.

Table 2 shows the classification of responders in the human study.

Tables 3 and 4 show markers from the human study which are preferably used for typing humans.

Table 5 illustrates for the human study predispositions present in subjects.

Table 6 shows markers from the human study, which are preferably used for typing humans.

Table 7 shows predictive markers for strength training response, which are preferably used for typing humans.

Table 8 shows predictive markers for endurance training response, which are preferably used for typing humans.

Table 9 shows predictive markers for either strength or endurance training response, which are preferably used for typing humans.

Table 10 shows the samples for the equine study.

Table 11 defines the ‘sex’ description used in Table 10.

Table 12 shows the sex distribution in the equine study.

Table 13 shows the top markers for Stayer versus Sprinter phenotype (n=32, 16 Stayer, 16 Sprinter), which are preferably used to type horses.

Table 14 shows markers discovered in humans that applicable to horses, and the closest genomic loci, which can be used to type horses.

Table 15 shows classifier calls for Sprinters and Stayers Table 16 shows probability scores for the equine study.

Table 17 shows classifier calls of naïve samples from young Thoroughbreds.

Table 18 shows the informative markers from the equine study, which are preferably used to type horses.

Tables 19 and 20 show the subjects for the human study.

Table 21 shows preferred genes for carrying out the invention.

Table 22 and 23 shows preferred markers from the equine study and the traits they relate to, which are preferably used to type horses.

Table 24 shows markers identified in the equine study, which are preferably used to type horses.

Table 25 shows markers identified in the human study, which are preferably used to type humans.

Table 26 shows another set of preferred genes for carrying out the invention.

Table 27 shows pathway analysis for genes locations for 171 chromosome interactions shared between the strength and endurance groups.

Table 28 shows pathway analysis for genes locations for the top 79 chromosome interactions which are unique to the endurance group.

Table 29 shows pathway analysis for genes locations for the top 79 chromosome interactions which are unique to the strength group.

Tables 30 to 32 show markers identified in the human study, which are preferably used to type humans.

To clarify the nomenclature used in the tables, including Table 30:

E_Trn refers to presence in Endurance Training

Str_Trn refers to presence in Strength Training

E_Ctrl refers to presence in Endurance Control (i.e. absence in Endurance Training)

Str_Ctrl refers to presence in Strength Control (i.e. absence in Strength Training)

Table 33 shows markers from an equine study, which are preferably used to type horses. In LS column: 1 means present in Sprinters, while (−1) means present in Stayers. The ‘Loop detection’ column is de facto decoding what +1 and −1 means in terms of detection.

Table 34 shows markers from a human study, which are preferably used to type humans.

Table 35 shows preferred markers from a horse study, which are preferably used to type horses.

Table 36 shows preferred markers from a human study, which are preferably used to type humans.

Table 37 shows an updated version of Table 30. The same markers are typed in this study in humans, preferably used to type humans.

Table 38 shows an updated version of Table 31. The same markers are typed in a human study and preferably used to type humans.

Table 39 shows an updated version of Table 32. The same markers are typed in a human study and preferably used to type humans.

Table 40 shows markers corresponding to those shown in FIG. 15, which are preferably used to type humans.

Table 41 shows updated results for Table 25, where the markers are from a human study and are preferably used to type human.

FIGS. 16 and 17 shows markers from a human study, which preferably can be used to type humans.

FIG. 18 shows markers from a horse study, which preferably can be used to type horses.

Preferred Methods

The following numbered paragraphs define preferred methods:

1. A process for detecting a chromosome state which represents a subgroup in a population comprising determining whether a chromosome interaction relating to that chromosome state is present or absent within a defined region of the genome, wherein said subgroup relates to physical performance in an individual; and

-   -   wherein said chromosome interaction has optionally been         identified by a method of determining which chromosomal         interactions are relevant to a chromosome state corresponding to         a physical performance subgroup of the population, comprising         contacting a first set of nucleic acids from subgroups with         different states of the chromosome with a second set of index         nucleic acids, and allowing complementary sequences to         hybridise, wherein the nucleic acids in the first and second         sets of nucleic acids represent a ligated product comprising         sequences from both the chromosome regions that have come         together in chromosomal interactions, and wherein the pattern of         hybridisation between the first and second set of nucleic acids         allows a determination of which chromosomal interactions are         specific to a physical performance subgroup; and     -   wherein the chromosome interaction either:

(i) corresponds to any one of the chromosome interactions shown in any of Tables 3, 7, 8, 9, 25 and 30; and/or

(ii) corresponds to any one of the chromosome interactions shown in any of Tables 13, 14, 18, 22, 23 and 24; and/or

(iii) is present in a 4,000 base region which comprises or which flanks (i) or (ii); and/or

(iv) is present in any one of the regions or genes listed in Table 21, 24, 25 or 30.

2. A process according to paragraph 1 wherein:

-   -   the individual is a human and the subgroup is a human subgroup     -   the individual is a horse and the subgroup is a horse subgroup,         and

wherein optionally:

(i) the process is carried out to determining physical performance ability, and/or

(ii) the process is carried out to detect responsiveness to a stimulus relating to physical performance, which is preferably physical training, and optionally strength or endurance training; and/or

(iii) the process is carried out to select an individual suitable for a physical activity, which is preferably a sport; and/or

(iv) the process is carried out to select a stimulus relating to physical performance to give to the individual, wherein said stimulus is a type of physical training.

3. A process according to paragraph 1 or 2 wherein a specific combination of chromosome interactions are typed:

(i) comprising all of the chromosome interactions represented in any of Tables 3, 7, 8, 9, 25 and 30 or any of Tables 13, 14, 18, 22, 23; and/or

(ii) comprising at least 10%, 20%, 50%, or 80% of the chromosome interactions in any of Tables 3, 7, 8, 9, 25 and 30 or any of Tables 13, 14, 18, 22, 23; and/or

(iii) which together are present in at least 10, 50 or 100 of the regions or genes listed in any of Tables 21, 24, 25 or 30; and/or

(iv) wherein at least 10, 50, 100, 150, 200 or 300 chromosome interactions are typed which are present in a 4,000 base region which comprises or which flanks the chromosome interactions represented in any of Tables 3, 7, 8, 9, 25 and 30 or any of Tables 13, 14, 18, 22, 23.

4. A process according to any one of the preceding paragraphs in which the chromosome interactions are typed:

-   -   in a sample from an individual, and/or     -   by detecting the presence or absence of a DNA loop at the site         of the chromosome interactions, and/or     -   detecting the presence or absence of distal regions of a         chromosome being brought together in a chromosome conformation,         and/or     -   by detecting the presence of a ligated nucleic acid which is         generated during said typing and whose sequence comprises two         regions each corresponding to the regions of the chromosome         which come together in the chromosome interaction, wherein         detection of the ligated nucleic acid is preferably by using         either:

(i) a probe that has at least 70% identity to any of the specific probe sequences mentioned in Table 24, 25 or 30, and/or (ii) by a primer pair which has at least 70% identity to any primer pair in Table 24, 25 or 30.

5. A process according to any one of the preceding paragraphs, wherein:

-   -   the second set of nucleic acids is from a larger group of         individuals than the first set of nucleic acids; and/or     -   the first set of nucleic acids is from at least 8 individuals;         and/or     -   the first set of nucleic acids is from at least 4 individuals         from a first subgroup and at least 4 individuals from a second         subgroup which is preferably non-overlapping with the first         subgroup.

6. A process according to any one of the preceding paragraphs wherein:

-   -   the second set of nucleic acids represents an unselected group;         and/or     -   wherein the second set of nucleic acids is bound to an array at         defined locations; and/or     -   wherein the second set of nucleic acids represents chromosome         interactions in least 100 different genes; and/or     -   wherein the second set of nucleic acids comprises at least 1,000         different nucleic acids representing at least 1,000 different         chromosome interactions; and/or     -   wherein the first set of nucleic acids and the second set of         nucleic acids comprise at least 100 nucleic acids with length 10         to 100 nucleotide bases.

7. A process according to any one of the preceding paragraphs, wherein the first set of nucleic acids is obtainable in a process comprising the steps of:—

-   -   (i) cross-linking of chromosome regions which have come together         in a chromosome interaction;     -   (ii) subjecting said cross-linked regions to cleavage,         optionally by restriction digestion cleavage with an enzyme; and     -   (iii) ligating said cross-linked cleaved DNA ends to form the         first set of nucleic acids (in particular comprising ligated         DNA).

8. A process according to any one of the preceding paragraphs:

-   -   wherein at least 10 to 50 different chromosome interactions are         typed, preferably in 10 to 50 different regions or genes         optionally as defined in Table 21, 24, 25 or 30; and/or     -   which is:

(i) carried out on a human or horse athlete; and/or

(ii) carried out as part of a training regime, preferably after the start of the training regime; and/or

(iii) carried out on a Thoroughbred horse, preferably a racing horse; or

(iv) carried out on a human individual of who is less than 20 years old or is carried out on a horse that is less than 18 months old, and/or

(v) which is carried out at multiple time points to assess physical performance characteristics at specific time points, wherein the process is optionally carried out at at least 3 time points, which are preferably at least 30 days apart from each other.

9. A process according to any one of the preceding paragraphs wherein said defined region of the genome:

(i) comprises a single nucleotide polymorphism (SNP); and/or

(ii) expresses a microRNA (miRNA); and/or

(iii) expresses a non-coding RNA (ncRNA); and/or

(iv) expresses a nucleic acid sequence encoding at least 10 contiguous amino acid residues; and/or

(v) expresses a regulating element; and/or

(vii) comprises a CTCF binding site.

10. A process according to any one of the preceding paragraphs:

-   -   which is carried out to identify an individual that is suited to         endurance training, and preferably the identified individual is         then subject to endurance training, which optionally occurs on         at least 100 days out of the next 365 days after the         identification; or     -   which is carried out to identify an individual that is suited to         strength training, and preferably the identified individual is         then subject to strength training, which optionally occurs on at         least 100 days out of the next 365 days after the         identification.

11. A process according to any one of the preceding paragraphs which is carried out to select the individual for racing.

12. A process according to any one of the preceding paragraphs which is carried out to identify or design a an agent that affects physical performance, wherein said process is used to detect whether a candidate agent is able to cause a change to a chromosome state which is associated with a different physical performance state; wherein

-   -   the chromosomal interaction is any specific interaction or         combination of interactions defined in any paragraph and/or is         present in any one of the regions or genes listed in Table 21,         24, 25 or 30; and/or     -   the change in chromosomal interaction is monitored using (i) a         probe that has at least 70% identity to any of the specific         probe sequences mentioned in Table 24, 25 or 30, and/or (ii) by         a primer pair which has at least 70% identity to any primer pair         in Table 24, 25 or 30.

13. A process according to paragraph 12 which comprises selecting a target based on detection of chromosome interactions, and preferably screening for a modulator of the target to identify an agent which affects physical performance, wherein said target is optionally a protein.

14. A process according to any one of the preceding paragraphs, wherein the typing or detecting comprises specific detection of the ligated product by quantitative PCR (qPCR) which uses primers capable of amplifying the ligated product and a probe which binds the ligation site during the PCR reaction, wherein said probe comprises sequence which is complementary to sequence from each of the chromosome regions that have come together in the chromosome interaction, wherein preferably said probe comprises:

an oligonucleotide which specifically binds to said ligated product, and/or

a fluorophore covalently attached to the 5′ end of the oligonucleotide, and/or

a quencher covalently attached to the 3′ end of the oligonucleotide, and

optionally

said fluorophore is selected from HEX, Texas Red and FAM; and/or

said probe comprises a nucleic acid sequence of length 10 to 40 nucleotide bases, preferably a length of 20 to 30 nucleotide bases.

15. A process according to any one of the proceeding paragraphs which further comprises:

-   -   producing a report on the physical performance characteristics         of the individual based on the results of the process, or     -   inputting the results of the process into a database, or     -   assigning a specific fitness or training regime to the         individual based on the results of the process, or     -   designing a specific fitness or training regime for the         individual based on the results of the process.

Specific Embodiments

The EpiSwitch™ platform technology detects epigenetic regulatory signatures of regulatory changes between normal and abnormal conditions at loci. The EpiSwitch™ platform identifies and monitors the fundamental epigenetic level of gene regulation associated with regulatory high order structures of human chromosomes also known as chromosome conformation signatures. Chromosome signatures are a distinct primary step in a cascade of gene deregulation. They are high order biomarkers with a unique set of advantages against biomarker platforms that utilize late epigenetic and gene expression biomarkers, such as DNA methylation and RNA profiling.

EpiSwitch™ Array Assay

The custom EpiSwitch™ array-screening platforms come in 4 densities of, 15K, 45K, 100K, and 250K unique chromosome conformations, each chimeric fragment is repeated on the arrays 4 times, making the effective densities 60K, 180K, 400K and 1 Million respectively.

Custom Designed EpiSwitch™ Arrays

The 15K EpiSwitch™ array can screen the whole genome including around 300 loci interrogated with the EpiSwitch™ Biomarker discovery technology. The EpiSwitch™ array is built on the Agilent SurePrint G3 Custom CGH microarray platform; this technology offers 4 densities, 60K, 180K, 400K and 1 Million probes. The density per array is reduced to 15K, 45K, 100K and 250K as each EpiSwitch™ probe is presented as a quadruplicate, thus allowing for statistical evaluation of the reproducibility. The average number of potential EpiSwitch™ markers interrogated per genetic loci is 50; as such the numbers of loci that can be investigated are 300, 900, 2000, and 5000.

EpiSwitch™ Custom Array Pipeline

The EpiSwitch™ array is a dual colour system with one set of samples, after EpiSwitch™ library generation, labelled in Cy5 and the other of sample (controls) to be compared/analyzed labelled in Cy3. The arrays are scanned using the Agilent SureScan Scanner and the resultant features extracted using the Agilent Feature Extraction software. The data is then processed using the EpiSwitch™ array processing scripts in R. The arrays are processed using standard dual colour packages in Bioconductor in R: Limma®. The normalisation of the arrays is done using the normalised Within Arrays function in Limma® and this is done to the on chip Agilent positive controls and EpiSwitch™ positive controls. The data is filtered based on the Agilent Flag calls, the Agilent control probes are removed and the technical replicate probes are averaged, in order for them to be analysed using Limma®. The probes are modelled based on their difference between the 2 scenarios being compared and then corrected by using False Discovery Rate. Probes with Coefficient of Variation (CV)<=30% that are <=−1.1 or =>1.1 and pass the p<=0.1 FDR p-value are used for further screening. To reduce the probe set further Multiple Factor Analysis is performed using the FactorMineR package in R.

* Note: LIMMA is Linear Models and Empirical Bayes Processes for Assessing Differential Expression in Microarray Experiments. Limma is an R package for the analysis of gene expression data arising from microarray or RNA-Seq.

The pool of probes is initially selected based on adjusted p-value, FC and CV<30% (arbitrary cut off point) parameters for final picking. Further analyses and the final list are drawn based only on the first two parameters (adj. p-value; FC).

Statistical Pipeline

EpiSwitch™ screening arrays are processed using the EpiSwitch™ Analytical Package in R in order to select high value EpiSwitch™ markers for translation on to the EpiSwitch™ PCR platform.

Step 1

Probes are selected based on their corrected p-value (False Discovery Rate, FDR), which is the product of a modified linear regression model. Probes below p-value <=0.1 are selected and then further reduced by their Epigenetic ratio (ER), probes ER have to be <=−1.1 or =>1.1 in order to be selected for further analysis. The last filter is a coefficient of variation (CV), probes have to be below <=0.3.

Step 2

The top 40 markers from the statistical lists are selected based on their ER for selection as markers for PCR translation. The top 20 markers with the highest negative ER load and the top 20 markers with the highest positive ER load form the list.

Step 3

The resultant markers from step 1, the statistically significant probes form the bases of enrichment analysis using hypergeometric enrichment (HE). This analysis enables marker reduction from the significant probe list, and along with the markers from step 2 forms the list of probes translated on to the EpiSwitch™ PCR platform.

The statistical probes are processed by HE to determine which genetic locations have an enrichment of statistically significant probes, indicating which genetic locations are hubs of epigenetic difference.

The most significant enriched loci based on a corrected p-value are selected for probe list generation. Genetic locations below p-value of 0.3 or 0.2 are selected. The statistical probes mapping to these genetic locations, with the markers from step 2, form the high value markers for EpiSwitch™ PCR translation.

Array Design and Processing Array Design

-   1. Genetic loci are processed using the SII software (currently     v3.2) to:     -   a. Pull out the sequence of the genome at these specific genetic         loci (gene sequence with 50 kb upstream and 20 kb downstream)     -   b. Define the probability that a sequence within this region is         involved in CCs     -   c. Cut the sequence using a specific RE     -   d. Determine which restriction fragments are likely to interact         in a certain orientation     -   e. Rank the likelihood of different CCs interacting together. -   2. Determine array size and therefore number of probe positions     available (x) -   3. Pull out x/4 interactions. -   4. For each interaction define sequence of 30 bp to restriction site     from part 1 and 30 bp to restriction site of part 2. Check those     regions aren't repeats, if so exclude and take next interaction down     on the list. Join both 30 bp to define probe. -   5. Create list of x/4 probes plus defined control probes and     replicate 4 times to create list to be created on array -   6. Upload list of probes onto Agilent Sure design website for custom     CGH array. -   7. Use probe group to design Agilent custom CGH array.

Array Processing

-   1. Process samples using EpiSwitch™ Standard Operating Procedure     (SOP) for template production. -   2. Clean up with ethanol precipitation by array processing     laboratory. -   3. Process samples as perAgilent SureTag complete DNA labelling     kit—Agilent Oligonucleotide Array-based CGH for Genomic DNA Analysis     Enzymatic labelling for Blood, Cells or Tissues -   4. Scan using Agilent C Scanner using Agilent feature extraction     software.

EpiSwitch™

EpiSwitch™ biomarker signatures demonstrate high robustness, sensitivity and specificity in the stratification of complex disease phenotypes. This technology takes advantage of the latest breakthroughs in the science of epigenetics, monitoring and evaluation of chromosome conformation signatures as a highly informative class of epigenetic biomarkers. Current research methodologies deployed in academic environment require from 3 to 7 days for biochemical processing of cellular material in order to detect CCSs. Those procedures have limited sensitivity, and reproducibility; and furthermore, do not have the benefit of the targeted insight provided by the EpiSwitch™ Analytical Package at the design stage.

EpiSwitch™ Array in Silica Marker Identification

CCS sites across the genome are directly evaluated by the EpiSwitch™ Array on clinical samples from testing cohorts for identification of all relevant stratifying lead biomarkers. The EpiSwitch™ Array platform is used for marker identification due to its high-throughput capacity, and its ability to screen large numbers of loci rapidly. The array used was the Agilent custom-CGH array, which allows markers identified through the in silico software to be interrogated.

EpiSwitch™ PCR

Potential markers identified by EpiSwitch™ Array are then validated either by EpiSwitch™ PCR or DNA sequencers (i.e. Roche 454, Nanopore MinION, etc.). The top PCR markers which are statistically significant and display the best reproducibility are selected for further reduction into the final EpiSwitch™ Signature Set, and validated on an independent cohort of samples. EpiSwitch™ PCR can be performed by a trained technician following a standardised operating procedure protocol established. All protocols and manufacture of reagents are performed under ISO 13485 and 9001 accreditation to ensure the quality of the work and the ability to transfer the protocols. EpiSwitch™ PCR and EpiSwitch™ Array biomarker platforms are compatible with analysis of both whole blood and cell lines. The tests are sensitive enough to detect abnormalities in very low copy numbers using small volumes of blood.

Example 1

This work concerns human epigenetic biomarkers which monitor physiological differences and predispositions associated with physical fitness training programs. Defined biomarkers have been discovered and evaluated to assist in the determination of epigenetic predisposition for either strength or endurance training, with monitoring after 4 weeks of mixed training and 8 weeks of specialized training.

Participant Recruitment:

Participants were recruited using posted fly paper, electronic newsletter, local print and radio media, targeted recruitment at local athletics clubs and word of mouth. To be eligible for enrolment to the study, participants were required to meet the following ‘performance’ criteria.

Group 1: strength athlete: Participant should be a regular weight-lifter. Example provided: 100 kg body mass and have a current accumulated total of 550 kg across; bench-press+squat+deadlift exercise.

Group 2: fitness athlete: Participant should be a regular fitness athlete. Example provided: current 10 km run time: <40 mins; or current 5 km run time <19 mins.

Group 3: sedentary non-athlete: has not been participating in sport or any form of structured exercise that causes physical exertion for >3 years.

Study Enrolment

Requisite criteria for potential enrolment were subjective (participant) reporting of athletic ability in order to meet one of three distinct phenotypes; 1) strength athlete 2) fitness athlete 3) sedentary non-athlete. Subsequently, eighty five (n=85) male participants aged 18-54 years, provided written informed consent prior to enrolling to the study. To confirm the meeting of enrolment criteria, comprehensive medical and athletic history were obtained before familiarisation protocol, blood sampling and performance tests were performed.

Familiarisation Protocol

Prior to physiological assessment, participants were acquainted with study procedures, personnel and provided with triaxial accelerometers (ActiGraph GT3X+, ActiGraph Corp), which were worn for 7-days in order to objectively determine participant physical activity, prior to physiological assessment.

Blood Sampling

Following overnight fast, morning blood samples were drawn from an antecubital vein by venepuncture, using 22 gauge needle into a 6 ml EDTA (BD Vacutainer®) blood tube. The blood tubes underwent 12 gentle inversions and immediately frozen at −80° C.

Anthropometrics

Height was determined using a portable stadiometer (Seca, Birmingham, U.K.). Body mass was measured to the nearest 0.1 kg by commercially available scales (body composition analyser TBF-300, Tanita, Tokyo, Japan). Total body fat percentage was calculated using bioelectrical impedance analysis (BIA) using a commercially available analyser (body composition analyser TBF-300, Tanita, Tokyo, Japan).

Strength Tests

For the 1RM tests, each subject attempted a weight that he believed could be lifted only once using maximum effort. The subject then added weight in increments of 2.2-4.5 kg until the heaviest load that could be successfully lifted once was determined. The subjects rested for approximately 3-5 minutes between attempts. The criterion for participant maximum strength was the combined 1RM max lifts (kg) for Squat+Bench Press+Deadlift exercises. Participant relative strength ratio was calculated as [Maximum Strength:Body Mass (kg:kg)]

-   -   Squat Exercise, 1 Rep Maximum (SQ 1RM)

During the SQ 1RM test, each lifter assumed an upright position, with the top of the bar not more than 3.0 cm below the top of the anterior deltoids. With both hands grasping the bar, the bar was removed from the rack, and the lifter moved back to assume a ready position, with knees extended, looking forward at the chief referee. On command, the lifter bent the knees and lowered the body in one smooth descent, until the top surface of the legs at the hip joint were lower than the top of the knees. The lifter then raised himself from the deepest point of the SQ to a standing position, with the knees extended. On command, the lifter replaced the weight back onto the rack with the aid of a spotter.

-   -   Bench Press, 1 Rep Maximum (BP 1RM)

The participant placed himself in a supine position, keeping his head, shoulders, and buttocks in constant contact with the weightlifting bench. The lifter's feet remained flat and motionless on the floor during the attempt. The participant received the bar at full arm's length from a spotter located behind the head of the bench. The bar was then lowered to the chest at a point 1-2 cm below the nipple line along the chest. When the bar became motionless on the chest, “press” command was issued and the participant extended his arms, returning the weight back to its starting position. Once the arms were completely extended, the chief referee gave a rack command, and the spotter aided the participant in returning the weight back to the racks on the bench.

Dead-lift, 1 Rep Maximum (DL 1RM)

For the DL 1RM, the participants feet and hands were spaced evenly from the centre of the bar and were allowed to be placed close to its centre (power style), or farther from the centre (sumo style). The participant lifted the bar vertically from the floor with one smooth motion until the knees and back extended the body to an erect position. When the knees became fully extended, upon command, and the participant lowered the bar to the floor.

Peak Aerobic Capacity Peak aerobic capacity ({dot over (V)}O₂ peak) was obtained indirect calorimetery on an electronically braked cycle ergometer (Velotron, RacerMate, Seattle, Wash., USA). Gas exchange was collected throughout the test using a metabolic cart (Moxus, AEI Technologies, Pittsburgh, Pa., USA). The test consisted unloaded pedalling for 1 min, followed by a step-wise increase to 50 W for 2 min. Subsequently, work rate was increased by 30 W min⁻¹ until the participant reached volitional fatigue (determined by the inability to maintain a minimum cadence above 60 rpm, blood lactate >7 mmol·l⁻¹, respiratory exchange ratio >1.15; reaching >90% of age predicted heart rate maximum). {dot over (V)}O₂ peak values were confirmed as the highest value during the final stage of the ramp protocol. Work rate (WR) was collected continuously throughout the test and peak aerobic power was calculated using the average WR from the last 30 s of the test.

Phenotype Confirmation

Group 1: Participants were required to meet at least the 90^(th) percentile for strength

STRENGHTPHENOTYPE: RelativeStrength Ratio* (RSR) >4.5 kg:kg

*RSR=[(SQ1RM kg+BP1RM kg+DL1RM kg)÷Body Mass (kg)]

Group 2: Participants were required to meet at least the 90^(th) percentile for aerobic capacity FITNESS PHENOTYPE: {dot over (V)}O₂ peak>51.4 ml·kg⁻²

Group 3: Participants were required to be on or below the 50^(th) percentile for strength and aerobic capacity

Strength: Relative Strength Ratio* (RSR)<3 kg:kg

Fitness: 50^(th) Percentile: {dot over (V)}O₂ peak<40.8 ml·kg⁻¹

Samples and Processing

The samples used in the study are shown in Table 1. The EpiSwitch™ template was prepared for each of the samples using the EpiSwitch™ extraction procedure. The 3C template library was quantified and the amount standardised to 1 ng/μl. A serial dilution was created and Nested PCR performed according to the EpiSwitch™ protocols.

Nested PCR was performed using the created serial dilutions for each sample for all 65 markers identified in part 2. For each marker the appropriate controls were included, these consisted of a no template control (NTC, all other reagents minus any DNA template) to monitor for any potential contamination of PCR reagents and a genomic control (negative control) to ensure the PCR products being detected are specific 3C products. The Nested PCR was analysed using high throughput capillary gel electrophoresis (LabChip GX Touch HT, Perkin Elmer) to identify and size the PCR products.

Training Response Annotations

The Nested PCR data was analysed using the retrospective annotation of end-point outcome for high and low response to exercise. To generate the annotations for each training group the individuals increase in physiological measurements due to undertaking the specified training regime, was ranked. The top 5 individuals in the ranking system were classed as High Responders for that training regime, the bottom 5 individuals were classed as Low responders (see table 2).

Results Overview

The analysis for part three of the project has been performed in two separate ways. The first is a direct analysis for predictive capability of 65 markers identified through the response analysis in part two and now screened in the third part of the project. The second is a parallel analysis of all the top 131 markers originally translated from EpiSwitch™ array of the high achieving Endurance and Strength Athletes. In this analysis the markers were evaluated strictly for their predictive potential using their baseline readouts and retrospective annotations of end-point outcome as High and Low response to specialized training by the end of 8 weeks of training. FIG. 1 provides a graphical representation and overview of the analysis. When compared, the two analysis streams have an overlap of 40.8%. The second analysis identifies 38 additional markers from the 131 original markers at the start of part 2 that are prime candidates to be predictive markers for training response. The overlap is shown in FIG. 2, with a circle marking the markers identified in the section 2 analysis stream that have not been processed. [FIG. 2 shows a Venn diagram of 80 potential markers identified in Analysis 2 compared to the 65 markers identified in part 2 and screened in part 3 based on exercise response]

Analysis 1

Analysis 1 was based on 3 comparisons. These three questions were designed to identify the markers from the 65 that were originally filtered on their responsiveness to mixed exercise and were predictive of an individual's outcome to specific training regimes or training in general. To that end the nested PCR data was analysed in three stratification groups:

-   -   1. High versus Low response (H/L) for Strength Training—to         identify markers that were predictive at baseline to the         end-point outcome of high or low response to Strength training.     -   2. High versus Low response (H/L) for Cardiovascular Endurance         Training—to identify markers that are predicative at baseline to         the end-point outcome of high or low response to Strength         training at baseline.     -   3. High versus Low (H/L) response independent of training,         grouping Strength and Endurance together—to identify markers         that are predictive at baseline to the end-point outcome of a         response to any/a training program at baseline.

The annotations of the outcome response to the training regimes at 8 weeks (after 4 weeks of specific cardio or strength training) were used to identify markers that are statistically significant for exercise response for the individual training regimes the third group looked at markers that were significant in both training programs.

To ensure the markers were predictive of training response H/L outcome and not just response markers, the binary nature of the marker at baseline and 8 weeks was investigated. Only markers that showed concordance between the two time points were selected. Filtering chromosome conformations that are stably detected before and after training that also show statistical significance between low and high response to the training programs selects for high quality markers that represent an inherent stable regulation framework in individuals that pre-disposes them to physiologically advance well or poorly to the final outcome of physical training of particular type.

Out of the 65 markers filtered through exercise response to 4-week of mixed training, 17 were found to be statistically significant. These are detailed in Table 3 and 4. These 17 markers represent a pool of high quality markers for the predisposition of training response in individuals at baseline (naïve) before training commences. The odds ratio shown in Table 3 is the measure of how strongly the absence and detection of the individual marker is associated with High/Low predicted outcome response to training in the sample population. An odds ratio of 1 indicates there is no difference between the two subpopulations (High and low response). The data strongly suggest that 17 discovered predictive markers are strongly associated with the successful outcome of training in the sample population with odds ratios of between 2 and 12.

Each marker was also individually assessed using Welch's t-test. This is a statistical test used to compare two sample populations and ascertain if the populations have equal means. An equal mean demonstrating that the two populations are not significant different. The p values shown in Table 5 are a measure of confidence that the inequality in the population means is due to actual differences and not be chance sampling.

A p value cut off of 0.3 is used to determine if the difference in detection of chromosome conformations are statistically significant. As will be seen in other literature this differs from the normally used 0.05 values. The 0.3 limit was experimentally derived to assure capturing markers that provide useful information gain, for example in the machine learning classifiers, strengthening the classifier performance.

The significant p values for each marker show the statistical significance of the odds ratios (OR) between training types in Table 3. The data in Tables 3 and 4 demonstrate quality and robustness of the 17 predictive markers identified.

Binary data from the marker OBD142_081.083_1.4x, as shown in Table 5 gives a useful example of both the higher detection rates between High and Low responders to exercise, in this case cardio endurance training and the predisposition already present at baseline before training commences. The data also represents a documented phenomenon of interference by mixed training causing disruption to the regulation before the chromatin regulation is reprogrammed back to its original predisposition state.

We identified the regulatory frame work for predictive advantage and predisposition of High response outcome in individuals being present at onset. The regulatory frame work in the low responders either preprogrammes to match that of the high responders, which they inherently possess already or fails to change at all. The markers represented in FIG. 3 are all marker for high response in strength training. FIG. 6. showing changes in detection for specific markers from baseline and after 8 weeks of training (4 weeks mixed, 4 weeks strength training), Y axis detection state 0=no detection, 1=detection, X axis 1=baseline, 2=8 weeks. FIG. 3A shows High responders is fixed with Low responders reprogramming causing the marker to become detectable due to the training programme. FIG. 3B shows High responders is fixed with Low responders reprogramming causing the marker to become undetectable due to the training programme. FIG. 3C shows High responders is fixed with Low responders also fixed, showing no modification of the chromatin landscape for this particular interaction.

Three of the 17 markers identified are anchored in the 3′ UTR of the DKK3 genetic locus (Table 6). It is evident that the DKK3 3′UTR is a hub of epigenetic control for this specific genetic locus with differential genomic architecture changing the regulation and accessibility creating predisposition for training response.

Analysis 2

The rationale for the second analysis was to look at the 131 markers screened at baseline in part 2 against retrospective annotations of end-point outcome of High or Low response to specialised training after 8 weeks. Many potential predictive markers may have been excluded in Analysis 1 as they were largely insensitive to the 4 weeks of mixed training. In contrast to analysis 1, which identified predictive markers with additional feature of responsiveness to mixed exercise, Analysis 2 was designed only to identify markers that were predictive of an individual's response to specific training programs.

Analysis 2 was based on the same three comparisons.

-   -   1. High versus Low response for Strength Training—to identify         markers that were predictive at baseline to the end-point         outcome of high or low response to Strength training at         baseline.     -   2. High versus Low response for Cardiovascular Endurance         Training—to identify markers that are predicative at baseline to         the end-point outcome of high or low response to Strength         training at baseline.     -   3. High versus Low response independent of training, grouping         Strength and Endurance together—to identify markers that are         predictive at baseline to the end-point outcome of a response to         any/a training program at baseline.

Welch's t—test was used to investigate the three comparisons. The test was cross validated by performing 1000 repeats with randomised sample selection. This gives 1000 different sample populations to test for the same 131 markers. Resampling and crossvalidation are used to ensure that the markers can generalise to an independent data set. The analysis output statistics for the predictive markers are shown in tables 7, 8 and 9. When duplications between the comparisons were removed the analysis identified 80 potential predictive markers. These 80 contained all 17 good predictive markers identified in Analysis 1.

FIG. 4 shows the analysis overlap. The circle on the left represents 38 additional predictive markers from Analysis 2. The circle in the middle shows the 42 overlapping predictive markers that have been investigated in part 2 and 3. These include the 17 markers detailed in Analysis 1. The circle on the right shows 23 markers investigated in part 2 and 3 that are Responsive markers to training. The composition of the 80 markers identified in Analysis two is shown in the Venn diagram in FIG. 5.

It is important to mention, that as an independent validation of the methodology in general and individual markers in particular, top significant markers with predictive powers for strength or endurance training outcome have been successfully translated into markers in an equine study. Based on the evolutionary conservation of genetic and epigenetic regulatory mechanisms underlying those markers, equine study of stayers and sprinters achieved 93.75% accuracy in classification of the development cohort of 32 (FIG. 6 which shows confusion matrix results).

Conclusions

-   -   1. Existing chromosome conformation signatures can be predictive         of later response outcome to training phenotypes. This is         consistent with a number of validated studies for development of         the predictive biomarkers to response to various treatments.     -   2. Statistically significant disseminating EpiSwitch™ markers         identified and evaluated in strength/endurance training for         human participants have been successfully translated into         statistically significant equine markers for stratification of         verified Sprinters and Stayers.     -   3. The 10 discovered markers classify between Sprinter and         Stayer phenotypes with an accuracy of 93.75% on the available         set of 32 validated samples.

Analysis 2 has identified 80 strong predictive markers, these include all the 17 predictive/response markers earlier reported in analysis 1 and an additional 38 markers that are predictive for H/L outcome to training response phenotypes when measured at baseline.

Summary

We have successfully identified and evaluated significant predictive biomarkers for H/L outcome of the strength/endurance training. These results achieve the objective of the project.

-   -   17 high quality robust predictive stable markers, with         sensitivity to mixed training, have been developed for use in         baseline prediction of an individual's response outcome to         specialized training regimes     -   A further 38 strictly predictive markers, independent of         response to mixed training, have been identified and evaluated         at baseline, for use in baseline prediction of an individual's         response outcome to specialized training regimes.

Example 2

Identification of validated signatures contain binary CCSs which are either present, or absent as conditional biomarkers of epigenetic regulation in equine individuals in strength or endurance training.

We identified CCSs biomarkers to successfully distinguish between Thoroughbreds, trained as either sprinters or a stayers. These markers can be used to determine predisposition and monitoring of young unraced Thoroughbreds as they are selected and undergo the training programs for sprinters and stayers. The markers are relevant to training potential, physiological monitoring and epigenetic reprogramming through training.

Project Approach

The top 50 EpiSwitch™ markers, identified from the work in human was translated into EpiSwitch™ designed Equine nested PCR assays and tested by the EpiSwitch™ PCR platform using Thoroughbreds with a defined phenotype: 1) sprinting 2) long-distance (Stayers) for evaluation of best disseminating markers for Sprinters and Stayers.

Samples

A total of 48 Samples were used as shown in Table 10:

-   -   16 Untrained young Thoroughbreds.     -   16 Trained Thoroughbreds classed as Sprinters.     -   16 Trained Thoroughbreds classed as Stayers.

The sex distribution between the sprinter and stayer sample types is balanced. The untrained male samples are skewed towards Colts against their castrated peers (Gelding), table 4. This skew will be accounted for in the biostatistical analysis.

Genome Conversion

The 131 markers identified on the Human array and translated to Nested PCR were translated from the GRCh38 Human Genome assembly to the EquCab2.0 Equine genome assembly using LiftOver (USSC). In total 114 of these were successfully translated. OBD's internal primer design application was used to design Nested primer sets for PCR, 65 of the 114 markers met the strict criteria for the successful primer design according to EpiSwitch™ operational procedures and methodology. The top 50 markers were selected for EpiSwitch™ equine nested PCR interrogation.

Nested PCR screening

The EpiSwitch™ template was prepared for each of the samples using the EpiSwitch™ extraction standard operation procedure. The 3C template library was quantified and the amount standardised to 1 ng/μl. A serial dilution was created and Nested PCR performed according to the EpiSwitch™ protocols

Nested PCR was performed using the created serial dilutions for each sample for all 50 markers selected. The Nested PCR was analysed using high throughput capillary gel electrophoresis (LabChip GX Touch HT, Perkin Elmer) to identify and size the PCR products. The data for the 16 Sprinters and 16 stayers was analysed using Boschloos' Test with resampling. The top 17 markers are shown in table 13.

In total, 17 of the 50 markers investigated were found to be statistically significant using a Boschloo p value cut off of 0.2. Importantly, this selection is produced using dilution individual titres, so each marker is produced by p-values based on the specific titres. Resampling of the data set was performed 100 times with a 66.7% partition, from the dataset of 32, 22 samples were selected at random and the statistical tests performed. This was repeated 100 times with the median result of this documented in table 13. These 17 markers represent interactions spaced around 16 genomic loci. The markers OBD154_045/047 and OBD154_049/051 are unique interactions that are across the same genomic location, see Table 4. The data show that a number of translated markers, discovered originally in a human cohort, are also applicable to horses.

MTFR1 (mitochondrial fission regulator 1) is notable from amongst identified loci as this was indicated in the most significant region from the Horse genetics for selection in thoroughbred Horses. Mitochondrial function and the management of reactive oxygen species are important for favorable exercise responses and therefore MTFR1 may impose strong selection pressure in Thoroughbreds by protection of mitochondria-rich tissue against oxidative stress. As such it is an excellent region for racing performance and endurance.

Classification

A classifier based on the Sprinter vs Stayer markers identified on the trained samples was developed to enable the classification of the untrained samples. Glmnet (Lasso and Elastic-Net Regularized Generalized Linear Models) was used to rank the markers in their ability to classify between sample types. The top 14 markers identified in Glmnet were then compared to the top 11 markers based on Boschloos' p value (Table 13). As shown in FIG. 7, 10 of the markers showed concordance and were shared between the two statistical analyses. The 10 concordant markers were selected to develop the classifier. XGBoost was used to model the markers and build a classifier.

The XGBoost model is an ensemble-based classifier that uses a series of weak classifying models to produce one overall strong model. In this gradient boosting methodology an initial model is created from the training data, a second model is then created that attempts to correct any errors in classification from the first model. This process is repeated n number of times to produce a final model that will classify the training set. A process of early stopping, ending the classifier build chain earlier then the initially set n value, is used to prevent the model over fitting the training set. A classification of the training set based on Sprinters and Stayers is shown in FIG. 6. Based on the 10 markers, the EpiSwitch™ test classifies well between Sprinters and Stayers, with an accuracy of 93.75%.

The probability calls of the 10 markers classifier are shown in Table 15. By default, a probability score >0.5 by the classifier is considered a call for a Sprinter, while <0.5 is considered a call for Stayer. On the basis of the results of classification in Table 15, the original probability scores (>0.5 for Sprinter, <0.5 for Stayer) were adjusted for quality classification calls on naïve samples from young Thoroughbreds. The established cut offs for the classifier calls are shown in Table 16.

The classifier was applied to the data for the naïve samples from young Thoroughbreds with the call results in Table 17. For 4 of the samples the classifier was unable to call the phenotype with high enough certainty and they fell into the unclassified limits. The remaining 12 samples were successfully called with a prediction of epigenetic profile conducive for the potential good Sprinter or Stayer. The 10 discovered markers classify between Sprinter and Stayer phenotypes with an accuracy of 93.75% on the available set of 32 validated samples.

Example 3 Further Work on the Human Study

A multinomial Glmnet regression analysis was performed based on three annotation groups, High responder, Medium responder and Low responder to each training type. Each CCS identified as predictive at baseline relative to training response outcomes was then compared across the time points for the sedentary controls to remove any CCS that showed variation due to effects other than the training under investigation. In total 18 CCS were identified as predictive for response to Strength training and 7 for response to Endurance training. Two of the CCS are shared between the training types (Mixed). Results are shown in tables 31 and 32.

Loop detected, or EpiSwitch marker present, are strict categories of predictive and stable markers for strength or endurance training. ‘High-responder’ markers are parts of epigenetic profile that conducive to very good physiological response to training program (using VO2 maximum and one-repetition maximum strength tests), i.e responders in our use of term. ‘Low-responders’ is the data analysis term that marks the stable predictive markers for individuals who will not change much their physiological performance after the training program (‘non-responders’).

Considering that ‘high response’ is the physiological data analysis term for ‘responder’ biomarker, and ‘low-response’ for ‘non-responders’, the majority of predictive response biomarkers are strength or endurance specific. However, several biomarkers reflect a dual function and provide information for good response in both endurance and strength.

The loop detected refers to array data, however Table 31 refers to strength and Table 32 refers to endurance based on PCR data. In regards to marker definitions and marker categories used by data analysis on array data:

Strength control: these are is just reference controls on the untrained side—readouts on the group of sedentary individuals before training at baseline. This is a physiological baseline control group.

Endurance control: same as above, but for endurance.

Strength training: these are reference controls, retrospective and ultimate positive controls, on high achievers in strength read out on the group of strength trained individuals after successful training. This is a physiological, positive control group.

Endurance training: same as before but for endurance.

This group of markers should be evaluated based on the following rules: the high responder markers as predictive and stable (from baseline onwards) responder markers, while low responder are the opposite side—predictive and stable markers of non-response to training. Generally predictive markers are specific for either strength or endurance as they were developed separately on either strength or endurance programmes and control groups. However there is some overlap, probably reflecting physiological overlap of the relevant regulatory networks—several markers are good predictive marker for good response in both strength or endurance training.

Overall Review of the Work

The original pool of genetic sites on the screening array was comprised of 1) inflammatory genes, 2) loci associated with micro-satellite differences in Thoroughbred horses and translated into humans. Thoroughbreds are highly inbred and the input of genetic component into phenotypical differences is highly limited in those subjects—this was considered the right model to search for any associations with epigenetic control sites, in terms of chromosome conformations. The fact that statistically significant sites are associated broadly with some of the well-known genes functionally linked to strength and endurance is the consequence of an independent selection. Importantly, screening of the potential candidates for chromosome conformation markers was driven by proprietary EpiSwitch annotations within non-coding parts of the genome within 100 kb windows of the referenced loci: upstream, downstream or encompassing the whole genes within the chromatin domain. At any part of the selection of CCS marker leads, no comparative assessment for any gene expression of any genes in the vicinity were made to assist the selection, thus excluding any link or correlation to gene expression changes of any of the genes and their known functional link to physical training outcomes.

Tables 34 to 36 show preferred powerful markers. The odds ratio shown in Table 36 is the measure of how strongly the absence and detection of the individual marker is associated with High/Low predicted outcome response to training in the sample population. An odds ratio of 1 indicates there is no difference between the two subpopulations (High and low response). The data strongly suggest that 17 discovered predictive markers are strongly associated with the successful outcome of training in the sample population with odds ratios of between 2 and 12.

Each marker was also individually assessed using Welch's t-test. This is a statistical test used to compare two sample populations and ascertain if the populations have equal means. An equal mean demonstrating that the two populations are not significant different. The p values shown are a measure of confidence that the inequality in the population means is due to actual differences and not be chance sampling.

We used a p value cut off of 0.3 to determine if the difference in detection of chromosome conformations are statistically significant. As will be seen in other literature this differs from the normally used 0.05 values. Through our previous projects, assay type and know-how the 0.3 limit was experimentally derived to assure capturing markers that provide useful information gain in the machine learning classifiers, strengthening the classifier performance. The significant p values for each marker show the statistical significance of the odds ratios (OR) between training types in this table. The data in this table demonstrates quality and robustness of the 17 predictive markers identified.

FIG. 15 is a VENN Diagram of Significant Markers for CV and Strength Baseline and 8 weeks. These markers are show in Table 40.

FIG. 16 shows baseline CV markers based on High and Low CV groups Exact P-values for association. These are the top 10 significant markers for the subjects at baseline based on the CV ranges. The range for Strength is a significant at baseline also. This indicates the close association between CV and strength ranges in these markers.

FIG. 17 shows baseline Strength markers based on high and Low Strength group Exact P-values for association. These are the top 20 significant markers for the subjects at baseline based on the Strength ranges. The range for CV is a significant at baseline also. This indicates the close association between CV and strength ranges in these markers.

FIG. 18 shows 10 Episwitch horse markers Identified from a UK cohort. The figure shows the genomic location in horses and the homologous region in the Human genome and the type of the marker: Sprinter or Stayer. The same 10 markers were used to classify the Singaporean Horses.

TABLE 1 Patient Sample ID Phenotype Response B16.3 Control — B17.3 Strength — B26.3 Cardio High B33.3 Cardio — B34.3 Cardio High B37.3 Strength High B38.3 Cardio Low B39.3 Strength High B40.3 Cardio High B43.3 Cardio Low B44.3 Cardio High B45.3 Strength Low B46.3 Strength High B51.3 Strength — B52.3 Control — B61.3 Cardio High B62.3 Strength Low B63.3 Excluded — B64.3 Strength Low B68.3 Cardio — B70.3 Strength High B71.3 Cardio Low B72.3 Strength High B73.3 Cardio Low B74.3 Strength — B76.3 Strength Low B77.3 Cardio Low B78.3 Strength — B79.3 Excluded — B80.3 Cardio — B83.3 Strength Low B85.3 Cardio —

TABLE 2 Individual Rank Label A 1 High response B 2 High response C 3 High response D 4 High response E 5 High response F 6 — G 7 — H 8 — I 9 — J 10 Low response K 11 Low response L 12 Low response M 13 Low response N 14 Low response

TABLE 3 Odds Marker Training Ratio OBD142_029.031_1x Presence in Endurance and Strength 7.2 OBD142_061.063_1.8x Presence in Endurance and Strength 8.2 OBD142_069.071_1.2x Presence in Endurance and Strength 8 OBD142_089.091_1x Presence in Endurance and Strength 2.9 OBD142_137.139_1.2x Presence in Endurance and Strength 8 OBD142_081.083_1.4x Presence in Endurance 6 OBD142_189.191_1x Presence in Endurance 4.5 OBD142_213.215_1.4x Presence in Endurance 2.25 OBD142_017.019_1.2x Presence in Strength 4 OBD142_037.039_1x Presence in Strength 12 OBD142_065.067_1x Presence in Strength 5 OBD142_133.135_1x Presence in Strength 4 OBD142_253.255_1.2x Presence in Strength 12 OBD142_353.355_1x Presence in Strength 9 OBD142_477.479_1x Presence in Strength 9 OBD142_181.183_1.4x Presence in Strength 2 OBD142_397.399_1x Presence in Strength 2

TABLE 4 Training type Marker Combined Cardio Strength OBD142_029.031_1x 0.01668097 0.066688 0.01613009 OBD142_061.063_1.8x 0.01851064 0.11741215 0.10680154 OBD142_069.071_1.2x 0.00255609 0.066688 0.05766889 OBD142_089.091_1x 0.12375267 0.40122897 0.18059725 OBD142_137.139_1.2x 0.06270144 0.11741215 0.18262433 OBD142_081.083_1.4x 0.13923948 0.070484 0.7999889 OBD142_189.191_1x 0.11969458 0.11741215 0.84528948 OBD142_213.215_1.4x 1 0.69409048 0.13523206 OBD142_017.019_1.2x 0.72495046 0.54542431 0.28124028 OBD142_037.039_1x 0.15251771 1 0.02525659 OBD142_065.067_1x 0.13191103 0.54542431 0.05766889 OBD142_133.135_1x 0.46156086 1 0.01613009 OBD142_253.255_1.2x 0.44960749 0.61010368 0.02421162 OBD142_353.355_1x 0.11969458 1 0.01615402 OBD142_477.479_1x 0.42751765 1 0.02525659 OBD142_181.183_1.4x 0.75595814 0.74070856 0.17780781 OBD142_397.399_1x 0.15163712 0.66842823 0.09667637

TABLE 5 Base 4 8 Response Trainee line weeks weeks to training B26 1 0 1 High B34 1 0 1 High B40 1 0 1 High B44 0 0 0 High B61 0 0 0 High B38 0 0 0 Low B43 0 0 0 Low B71 0 0 0 Low B73 0 1 0 Low B77 0 1 0 Low

TABLE 6 Marker High or low response Training type OBD142_061.063_1.8x High Both OBD142_069.071_1.2x High Both OBD142_065.067_1x High Strength

Rank Rank Rank Mean p Median Marker with Dilution Marker Freq Sum Mean Median value p value OBD142_437.439_1.2x OBD142_437.439 1000 198 1.98 2 0.01576 0.01562 OBD142_025.027_1x OBD142_025.027 1000 1224.5 12.245 8.5 0.08678 0.09375 OBD142_417.419_1x OBD142_417.419 1000 1369 13.69 13 0.09328 0.12500 OBD142_517.519_1.2x OBD142_517.519 1000 1251.5 12.515 13 0.09312 0.12500 OBD142_065.067_1x OBD142_065.067 971 3903 39.03 35.5 0.20758 0.13696 OBD142_513.515_1.2x OBD142_513.515 971 3903 39.03 35.5 0.20758 0.13696 OBD142_017.019_1x OBD142_017.019 977 4446 44.46 40 0.23382 0.28125 OBD142_029.031_1x OBD142_029.031 972 4681.5 46.815 40.5 0.23992 0.28125 OBD142_069.071_1.2x OBD142_069.071 972 5103.5 51.035 40 0.26566 0.28125 OBD142_085.087_1.2x OBD142_085.087 972 4667 46.67 41 0.24252 0.28125 OBD142_093.095_1x OBD142_093.095 1000 3945 39.45 40 0.22246 0.28125 OBD142_117.119_1.2x OBD142_117.119 1000 4206.5 42.065 38.5 0.23621 0.28125 OBD142_125.127_1.2x OBD142_125.127 977 4446 44.46 40 0.23382 0.28125 OBD142_157.159_1.4x OBD142_157.159 1000 3707.5 37.075 38 0.22324 0.28125 OBD142_233.235_1.4x OBD142_233.235 1000 3707.5 37.075 38 0.22324 0.28125 OBD142_285.287_1.4x OBD142_285.287 975 4749 47.49 37.75 0.24953 0.28125 OBD142_325.327_1.4x OBD142_325.327 1000 4206.5 42.065 38.5 0.23621 0.28125 OBD142_449.451_1x OBD142_449.451 1000 3738 37.38 38.25 0.21652 0.28125 OBD142_461.463_1.4x OBD142_461.463 972 4667 46.67 41 0.24252 0.28125 OBD142_469.471_1x OBD142_469.471 975 4749 47.49 37.75 0.24953 0.28125 OBD142_133.135_1x OBD142_133.135 504 14009 140.09 86.5 0.60112 0.34375 OBD142_181.183_1.4x OBD142_181.183 504 14009 140.09 86.5 0.60112 0.34375 OBD142_397.399_1x OBD142_397.399 504 14009 140.09 86.5 0.60112 0.34375 OBD142_253.255_1.2x OBD142_253.255 867 7643 76.43 109.25 0.62216 0.34375 OBD142_181.183_1.4x OBD142_181.183 504 14009 140.09 86.5 0.60112 0.34375 OBD142_037.039_1x OBD142_037.039 779 8626.5 86.265 113 0.35984 0.45312 OBD142_353.355_1x OBD142_353.355 699 8585.5 85.855 113 0.35078 0.45312

Table 7 shows predictive markers for strength training response, which are preferably used for typing humans. (Present in strength training in humans)

Rank Rank Rank Mean p Median Marker with Dilution Marker Freq Sum Mean Median value p value OBD142_005.007_1x OBD142_005.007 527 12594.5 125.945 76.5 0.57000 0.28906 OBD142_009.011_1.4x OBD142_009.011 737 9784 97.84 44.5 0.44750 0.18750 OBD142_025.027_1.2x OBD142_025.027 1000 11604 116.04 42 0.53687 0.18750 OBD142_029.031_1.4x OBD142_029.031 1000 2760.5 27.605 38 0.13594 0.18750 OBD142_041.043_1.2x OBD142_041.043 737 9784 97.84 44.5 0.44750 0.18750 OBD142_045.047_1x OBD142_045.047 525 13251.5 132.515 77.5 0.60297 0.28906 OBD142_057.059_1.8x OBD142_057.059 715 11959.5 119.595 51.5 0.55312 0.18750 OBD142_061.063_1.4x OBD142_061.063 814 10698.5 106.985 44.5 0.49625 0.18750 OBD142_065.067_1.2x OBD142_065.067 1000 859.5 8.595 9.5 0.05469 0.07031 OBD142_069.071_1.2x OBD142_069.071 967 10625.5 106.255 43 0.48812 0.18750 OBD142_081.083_1.4x OBD142_081.083 1000 2686 26.86 34 0.13008 0.18750 OBD142_097.099_1.8x OBD142_097.099 1000 11838 118.38 51.5 0.54500 0.18750 OBD142_101.103_1x OBD142_101.103 1000 5050 50.5 70 0.21125 0.28906 OBD142_109.111_1.2x OBD142_109.111 1000 11604 116.04 42 0.53687 0.18750 OBD142_121.123_1.8x OBD142_121.123 814 10698.5 106.985 44.5 0.49625 0.18750 OBD142_133.135_1.8x OBD142_133.135 737 9784 97.84 44.5 0.44750 0.18750 OBD142_137.139_1.2x OBD142_137.139 1000 3052 30.52 39 0.14414 0.18750 OBD142_141.143_1.4x OBD142_141.143 737 9784 97.84 44.5 0.44750 0.18750 OBD142_145.147_1.4x OBD142_145.147 523 12431.5 124.315 81.5 0.56711 0.28906 OBD142_153.155_1.4x OBD142_153.155 1000 914 9.14 10 0.05781 0.07031 OBD142_157.159_1.4x OBD142_157.159 514 13293.5 132.935 83.5 0.60250 0.28906 OBD142_165.167_1x OBD142_165.167 1000 4818.5 48.185 69.5 0.20031 0.28906 OBD142_185.187_1.4x OBD142_185.187 1000 3161 31.61 39 0.15117 0.18750 OBD142_189.191_1x OBD142_189.191 1000 2760.5 27.605 38 0.13594 0.18750 OBD142_197.199_1.4x OBD142_197.199 1000 2795 27.95 38 0.13711 0.18750 OBD142_201.203_1.4x OBD142_201.203 1000 2903.5 29.035 38.5 0.14180 0.18750 OBD142_213.215_1.4x OBD142_213.215 151 19515.5 195.155 212 0.90047 1.00000 OBD142_233.235_1.2x OBD142_233.235 505 12737 127.37 81.5 0.57758 0.28906 OBD142_241.243_1x OBD142_241.243 1000 2820.5 28.205 38 0.13828 0.18750 OBD142_253.255_1.2x OBD142_253.255 1000 5334.5 53.345 70 0.22125 0.28906 OBD142_257.259_1.2x OBD142_257.259 1000 11995.5 119.955 51.5 0.55312 0.18750 OBD142_261.263_1x OBD142_261.263 1000 5144 51.44 69.5 0.21031 0.28906 OBD142_265.267_1.4x OBD142_265.267 967 9975.5 99.755 41.5 0.46375 0.18750 OBD142_273.275_1.4x OBD142_273.275 962 12527 125.27 51.5 0.58562 0.18750 OBD142_277.279_1.2x OBD142_277.279 1000 3060 30.6 38.5 0.14766 0.18750 OBD142_297.299_1.2x OBD142_297.299 1000 847.5 8.475 9.5 0.05531 0.07031 OBD142_309.311_1.4x OBD142_309.311 806 9550 95.5 42 0.43937 0.18750 OBD142_313.315_1x OBD142_313.315 1000 2760.5 27.605 38 0.13594 0.18750 OBD142_321.323_1.2x OBD142_321.323 1000 11995.5 119.955 51.5 0.55312 0.18750 OBD142_325.327_1.2x OBD142_325.327 1000 4958.5 49.585 69.5 0.20344 0.28906 OBD142_329.331_1.4x OBD142_329.331 1000 2795 27.95 38 0.13711 0.18750 OBD142_337.339_1x OBD142_337.339 817 10759.5 107.595 43 0.49625 0.18750 OBD142_357.359_1.4x OBD142_357.359 962 12527 125.27 51.5 0.58562 0.18750 OBD142_361.363_1.2x OBD142_361.363 932 11406.5 114.065 43 0.52875 0.18750 OBD142_373.375_1x OBD142_373.375 1000 2903.5 29.035 38.5 0.14180 0.18750 OBD142_393.395_1.2x OBD142_393.395 1000 921.5 9.215 10.5 0.05781 0.07031 OBD142_401.403_1x OBD142_401.403 1000 2820.5 28.205 38 0.13828 0.18750 OBD142_405.407_1x OBD142_405.407 537 11739.5 117.395 73.5 0.52570 0.28906 OBD142_413.415_1.2x OBD142_413.415 638 10473 104.73 45.5 0.48812 0.18750 OBD142_433.435_1x OBD142_433.435 1000 2969.5 29.695 39 0.14297 0.18750 OBD142_437.439_1x OBD142_437.439 1000 5144 51.44 69.5 0.21031 0.28906 OBD142_445.447_1.2x OBD142_445.447 752 10351.5 103.515 45 0.48000 0.18750 OBD142_457.459_1x OBD142_457.459 1000 3016 30.16 38.5 0.14414 0.18750 OBD142_469.471_1.2x OBD142_469.471 1000 2829 28.29 38.5 0.13594 0.18750 OBD142_477.479_1.2x OBD142_477.479 752 10351.5 103.515 45 0.48000 0.18750 OBD142_489.491_1x OBD142_489.491 937 9975.5 99.755 41.5 0.46375 0.18750 OBD142_501.503_1x OBD142_501.503 537 11739.5 117.395 73.5 0.52570 0.28906 OBD142_509.511_1.8x OBD142_509.511 970 11725.5 117.255 43.25 0.54500 0.18750 OBD142_517.519_1x OBD142_517.519 1000 914 9.14 10 0.05781 0.07031

Table 8 shows predictive markers for endurance training response, which are preferably used for typing humans. (Present in endurance training in humans).

Rank Rank Rank Mean p Median Marker with Dilution Marker Freq Sum Mean Median value p value OBD142_005.007_1x OBD142_005.007 731 10275.5 102.755 71.5 0.33252 0.23486 OBD142_017.019_1x OBD142_017.019 657 8644 86.44 57.5 0.28238 0.23486 OBD142_025.027_1.2x OBD142_025.027 1000 1075 10.75 6.25 0.04110 0.03613 OBD142_029.031_1x OBD142_029.031 971 4960.5 49.605 39.5 0.17457 0.13770 OBD142_041.043_1.4x OBD142_041.043 837 9882.5 98.825 83.75 0.33162 0.28271 OBD142_045.047_1.2x OBD142_045.047 817 7944 79.44 52 0.25580 0.19141 OBD142_057.059_1.4x OBD142_057.059 707 8843 88.43 56.25 0.28852 0.19141 OBD142_061.063_1.8x OBD142_061.063 906 5038 50.38 28.5 0.16971 0.09229 OBD142_065.067_1x OBD142_065.067 992 2771.5 27.715 18.25 0.10043 0.05800 OBD142_069.071_1.2x OBD142_069.071 998 2877.5 28.775 16.25 0.10248 0.05800 OBD142_085.087_1.4x OBD142_085.087 783 13339.5 133.395 88.75 0.44247 0.28271 OBD142_089.091_1x OBD142_089.091 214 21704.5 217.045 221.25 0.70459 0.58105 OBD142_097.099_1.8x OBD142_097.099 986 4753 47.53 36.75 0.16534 0.13770 OBD142_101.103_1x OBD142_101.103 692 10572.5 105.725 74.75 0.34013 0.26685 OBD142_113.115_1.2x OBD142_113.115 633 11276 112.76 76.75 0.36933 0.26685 OBD142_117.119_1.2x OBD142_117.119 586 11545 115.45 80.75 0.36613 0.26685 OBD142_121.123_1.8x OBD142_121.123 785 12882.5 128.825 91.75 0.42484 0.28271 OBD142_137.139_1.2x OBD142_137.139 811 8486.5 84.865 55 0.28375 0.19751 OBD142_145.147_1.2x OBD142_145.147 779 9565.5 95.655 67 0.31244 0.23486 OBD142_153.155_1.2x OBD142_153.155 996 2110.5 21.105 13.5 0.08214 0.07031 OBD142_157.159_1.4x OBD142_157.159 901 4935 49.35 24 0.16512 0.09229 OBD142_181.183_1.2x OBD142_181.183 726 13631.5 136.315 88.5 0.44859 0.28271 OBD142_185.187_1.4x OBD142_185.187 800 7477.5 74.775 54.5 0.24398 0.19141 OBD142_189.191_1.2x OBD142_189.191 990 2092.5 20.925 13.75 0.08116 0.07031 OBD142_197.199_1.4x OBD142_197.199 806 10234 102.34 88 0.34598 0.28271 OBD142_201.203_1.4x OBD142_201.203 752 10967 109.67 93 0.36080 0.28271 OBD142_225.227_1.2x OBD142_225.227 910 9781 97.81 83.75 0.32891 0.28271 OBD142_233.235_1.2x OBD142_233.235 886 6386 63.86 29.75 0.21925 0.09229 OBD142_241.243_1x OBD142_241.243 883 4360.5 43.605 30.5 0.15074 0.11284 OBD142_253.255_1.2x OBD142_253.255 986 2287.5 22.875 18 0.08839 0.09229 OBD142_257.259_1.2x OBD142_257.259 961 6557.5 65.575 39.75 0.22005 0.13770 OBD142_261.263_1x OBD142_261.263 894 5356.5 53.565 26.25 0.17615 0.09229 OBD142_273.275_1.4x OBD142_273.275 864 10216.5 102.165 88 0.34298 0.28271 OBD142_309.311_1.2x OBD142_309.311 762 10278 102.78 64 0.33810 0.23486 OBD142_321.323_1x OBD142_321.323 958 5677.5 56.775 42.25 0.18968 0.13770 OBD142_325.327_1.4x OBD142_325.327 958 4037 40.37 20.75 0.13814 0.09229 OBD142_329.331_1x OBD142_329.331 943 6060.5 60.605 45 0.19830 0.13770 OBD142_349.351_1x OBD142_349.351 689 10674 106.74 74.75 0.35113 0.24731 OBD142_353.355_1x OBD142_353.355 743 9010.5 90.105 65.5 0.29709 0.23486 OBD142_361.363_1.2x OBD142_361.363 741 9202 92.02 59.5 0.30628 0.23486 OBD142_373.375_1x OBD142_373.375 952 5814 58.14 41.75 0.19707 0.13770 OBD142_389.391_1x OBD142_389.391 855 10445 104.45 84.75 0.35071 0.28271 OBD142_393.395_1.2x OBD142_393.395 961 5026 50.26 30.75 0.16382 0.10229 OBD142_405.407_1x OBD142_405.407 661 9730.5 97.305 74.25 0.32788 0.26685 OBD142_433.435_1x OBD142_433.435 663 10280.5 102.805 69 0.33826 0.23486 OBD142_437.439_1.2x OBD142_437.439 679 11065 110.65 77.25 0.36270 0.25977 OBD142_445.447_1.2x OBD142_445.447 959 5236.5 52.365 39 0.18092 0.13770 OBD142_461.463_1.4x OBD142_461.463 946 6240 62.4 36.5 0.21435 0.13770 OBD142_469.471_1.2x OBD142_469.471 832 8858.5 88.585 56.75 0.29436 0.19917 OBD142_477.479_1x OBD142_477.479 629 12148 121.48 74.75 0.40365 0.25977 OBD142_489.491_1.2x OBD142_489.491 748 7759.5 77.595 58.5 0.24931 0.20083 OBD142_497.499_1.2x OBD142_497.499 675 10138.5 101.385 77.25 0.33286 0.26331 OBD142_509.511_1.8x OBD142_509.511 988 4712 47.12 33 0.16110 0.10229 OBD142_521.523_1.4x OBD142_521.523 747 13280 132.8 93.5 0.44187 0.28271

Table 9 shows predictive markers for either strength or endurance training response, which are preferably used for typing humans. (Present in strength and endurance training in humans).

TABLE 10 Patient Sample ID Basic Annotation Sex Brigand Horse - Sprinter Gelding Brigand Horse - Sprinter Gelding Headway Horse - Sprinter Colt Headway Horse - Sprinter Colt Barton Mills Horse - Sprinter Colt Barton Mills Horse - Sprinter Colt Muthmir Horse - Sprinter Gelding Muthmir Horse - Sprinter Gelding One Master Horse - Sprinter Filly One Master Horse - Sprinter Filly Move Swiftly Horse - Sprinter Filly Move Swiftly Horse - Sprinter Filly Island of life Horse - Sprinter Filly Island of life Horse - Sprinter Filly Juthoor Horse - Sprinter Colt Juthoor Horse - Sprinter Colt Pretty Baby Horse - Sprinter Filly Pretty Baby Horse - Sprinter Filly Robin Weathers Horse - Sprinter Colt Robin Weathers Horse - Sprinter Colt Beshaayir Horse - Sprinter Filly Beshaayir Horse - Sprinter Filly Mashaheer Horse - Sprinter Gelding Mashaheer Horse - Sprinter Gelding Mubtasim Horse - Sprinter Gelding Mubtasim Horse - Sprinter Gelding Tasleet Horse - Sprinter Colt Tasleet Horse - Sprinter Colt Important Mission Horse - Sprinter Gelding Important Mission Horse - Sprinter Gelding Algaffaal Horse - Sprinter Colt Algaffaal Horse - Sprinter Colt Carpio Horse - Untrained Colt Carpio Horse - Untrained Colt ex Donnellys Hollow Horse - Untrained Filly ex Donnellys Hollow Horse - Untrained Filly ex Marika Horse - Untrained Colt ex Marika Horse - Untrained Colt Narina Horse - Untrained Filly Narina Horse - Untrained Filly Setenta Horse - Untrained Colt Setenta Horse - Untrained Colt To Be Wild Horse - Untrained Colt To Be Wild Horse - Untrained Colt Starkers Horse - Untrained Filly Starkers Horse - Untrained Filly Soloist Horse - Untrained Filly Soloist Horse - Untrained Filly Field Gun Horse - Untrained Gelding Field Gun Horse - Untrained Gelding ex No Song Horse - Untrained Colt ex No Song Horse - Untrained Colt ex Celtic Lynn Horse - Untrained Colt ex Celtic Lynn Horse - Untrained Colt flare of firelight Horse - Untrained Colt flare of firelight Horse - Untrained Colt Second Thought Horse - Untrained Colt Second Thought Horse - Untrained Colt Dance Pearl Horse - Untrained Filly Dance Pearl Horse - Untrained Filly ex Yosoldina Horse - Untrained Filly ex Yosoldina Horse - Untrained Filly Queen of Mean Horse - Untrained Colt Queen of Mean Horse - Untrained Colt Al Muffrih Horse - Stayer Stayer Al Muffrih Horse - Stayer Stayer Dal Harraild Horse - Stayer Gelding Dal Harraild Horse - Stayer Gelding Humble Hera Horse - Stayer Colt Humble Hera Horse - Stayer Colt Istanbul Sultan Horse - Stayer Gelding Istanbul Sultan Horse - Stayer Gelding Young Rascal Horse - Stayer Colt Young Rascal Horse - Stayer Colt Give & Take Horse - Stayer Filly Give & Take Horse - Stayer Filly Alexana Horse - Stayer Filly Alexana Horse - Stayer Filly Call To Mind Horse - Stayer Colt Call To Mind Horse - Stayer Colt Cristal Spirit Horse - Stayer Gelding Cristal Spirit Horse - Stayer Gelding Heart of Grace Horse - Stayer Filly Heart of Grace Horse - Stayer Filly Mam'Selle Horse - Stayer Filly Mam'Selle Horse - Stayer Filly Smashed Horse - Stayer Colt Smashed Horse - Stayer Colt Dramatic Queen Horse - Stayer Filly Dramatic Queen Horse - Stayer Filly Nicklaus Horse - Stayer Colt Nicklaus Horse - Stayer Colt Reverend Jacobs Horse - Stayer Gelding Reverend Jacobs Horse - Stayer Gelding The Grand Visir Horse - Stayer Colt The Grand Visir Horse - Stayer Colt

TABLE 11 Sex Description Colt Male horse less than three years old Gelding Castrated Male horse less than three years old Filly Female horse less than three years old

TABLE 12 Untrained Sprinter Stayer Colt 9 6 7 Gelding 1 5 4 Filly 6 5 5

N Marker Exact_Boschloo_p.value Median_Boshloo Dilution Type 1 OBD154_125/OBD154_127 0.00631 0.037817955 OBD154_125/OBD154_127_1:2x Present in Sprinter 2 OBD154_085/OBD154_087 0.03886 0.088156223 OBD154_085/OBD154_087_1:2x Present in Sprinter 3 OBD154_157/OBD154_159 0.03886 0.088156223 OBD154_157/OBD154_159_1:2x Present in Stayer 4 OBD154_013/OBD154_015 0.05011 0.13798237 OBD154_013/OBD154_015_1x Present in Sprinter 5 OBD154_245/OBD154_247 0.05011 0.13798237 OBD154_245/OBD154_247_1x Present in Sprinter 6 OBD154_229/OBD154_231 0.05419 0.239017755 OBD154_229/OBD154_231_1x Present in Sprinter 7 OBD154_093/OBD154_095 0.07514 0.239017755 OBD154_093/OBD154_095_1:2x Present in Sprinter 8 OBD154_049/OBD154_051 0.11993 0.243710751 OBD154_049/OBD154_051_1:4x Present in Sprinter 9 OBD154_201/OBD154_203 0.11993 0.243710751 OBD154_201/OBD154_203_1:2x Present in Stayer 10 OBD154_041/OBD154_043 0.12508 0.239017755 OBD154_041/OBD154_043_1:4x Present in Stayer 11 OBD154_073/OBD154_075 0.12508 0.239017755 OBD154_073/OBD154_075_1x Present in Stayer 12 OBD154_205/OBD154_207 0.12508 0.239017755 OBD154_205/OBD154_207_1:2x Present in Sprinter 13 OBD154_009/OBD154_011 0.18007 0.239017755 OBD154_009/OBD154_011_1:2x Present in Sprinter 14 OBD154_045/OBD154_047 0.18007 0.287077538 OBD154_045/OBD154_047_1x Present in Stayer 15 OBD154_141/OBD154_143 0.18007 0.287077538 OBD154_141/OBD154_143_1x Present in Sprinter 16 OBD154_165/OBD154_167 0.18007 0.287077538 OBD154_165/OBD154_167_1x Present in Sprinter 17 OBD154_213/OBD154_215 0.18007 0.265394144 OBD154_213/OBD154_215_1:2x Present in Stayer

Table 13 shows the top markers for Stayer versus Sprinter phenotype (n=32, 16 Stayer, 16 Sprinter), which are preferably used to type horses.

Nearest Marker Gene/loci Type OBD154_045/OBD154_047 MC1R/ Present in Stayer NM_001081945 OBD154_073/OBD154_075 MIRLET7A-2/ Present in Stayer PPARA OBD154_009/OBD154_011 MIR1898 Present in Sprinter OBD154_041/OBD154_043 TAGLN/ Present in Stayer MIR125B OBD154_093/OBD154_095 MIR1248/TFRC Present in Sprinter OBD154_085/OBD154_087 SYNJ2BP Present in Sprinter OBD154_013/OBD154_015 AMPP/ARNTL Present in Sprinter OBD154_049/OBD154_051 MC1R/ Present in Sprinter NM_001081945 OBD154_125/OBD154_127 CCDC146 Present in Sprinter OBD154_165/OBD154_167 MIR17 Present in Sprinter OBD154_201/OBD154_203 GSN Present in Stayer OBD154_229/OBD154_231 ALPHA4GNT Present in Sprinter OBD154_213/OBD154_215 BMP7 Present in Stayer OBD154_205/OBD154_207 S100G/NROB1 Present in Sprinter OBD154_157/OBD154_159 EEF1A1 Present in Stayer OBD154_245/OBD154_247 MIR218 Present in Sprinter OBD154_141/OBD154_143 NME1/SRSF1 Present in Sprinter Table 14 shows markers discovered in humans that applicable to horses, and the closest genomic loci, which can be used to type horses.

TABLE 15 Sample ID Horse Name Phenotype Probability Comments Holo009 One Master Sprinter 0.887 Correct Holo013 Island of life Sprinter 0.962 Correct Holo019 Robin Weathers Sprinter 0.321 Misclassified Holo017 Pretty Baby Sprinter 0.872 Correct Holo015 Juthoor Sprinter 0.974 Correct Holo023 Masha heer Sprinter 0.960 Correct Holo003 Headway Sprinter 0.852 Correct Holo011 Move Swiftly Sprinter 0.993 Correct Holo007 Muthmir Sprinter 0.732 Correct Holo031 Algaffaal Sprinter 0.958 Correct Holo005 Barton Mills Sprinter 0.974 Correct Holo021 Beshaayir Sprinter 0.961 Correct Holo001 Brigand Sprinter 0.991 Correct Holo025 Mubtasim Sprinter 0.835 Correct Holo027 Tasleet Sprinter 0.958 Correct Holo029 Important Mission Sprinter 0.670 Correct Holo065 Al Muffrih Stayer 0.150 Correct Holo077 Alexana Stayer 0.014 Correct Holo069 Humble Hero Stayer 0.550 Misclassified Holo091 Nicklaus Stayer 0.086 Correct Holo071 Istanbul Sultan Stayer 0.265 Correct Holo075 Give & Take Stayer 0.271 Correct Holo083 Heart of Grace Stayer 0.032 Correct Holo067 Dal Harraild Stayer 0.298 Correct Holo089 Dramatic Queen Stayer 0.027 Correct Holo079 Call To Mind Stayer 0.032 Correct Holo095 The Grand Visir Stayer 0.283 Correct Holo081 Cristal Spirit Stayer 0.032 Correct Holo093 Reverend Jacobs Stayer 0.095 Correct Holo087 Smashed Stayer 0.167 Correct Holo073 Young Rascal Stayer 0.166 Correct Holo085 Mam'Selle Stayer 0.014 Correct

TABLE 16 Probability Score Classifier Call <0.3 Stayer 0.31-0.69 Unclassified >0.7 Sprinter

TABLE 17 Sample Horse Name Probability Call Holo053 ex Celtic Lynn 0.383045197 Unclassified Holo045 Starkers 0.165671632 Stayer Holo035 ex Donnellys Hollow 0.549999774 Unclassified Holo051 ex No Song 0.973659277 Sprinter Holo057 Second Thought 0.271233022 Stayer Holo059 Dance Pearl 0.549999774 Unclassified Holo039 Narina 0.871761441 Sprinter Holo043 To Be Wild 0.092756219 Stayer Holo061 ex Yosoldina 0.031833708 Stayer Holo055 Flare of Firelight 0.889145136 Sprinter Holo063 Queen of Mean 0.004074222 Stayer Holo047 Soloist 0.025709741 Stayer Holo033 Carpio 0.0436165 Stayer Holo041 Setenta 0.549999774 Unclassified Holo049 Field Gun 0.094702385 Stayer Holo037 ex Marika 0.882559121 Sprinter

Marker Exact_Boschloo_p.value Type OBD154_001/OBD154_003_1:2x 0.597203758 Present in Sprinter OBD154_009/OBD154_011_1:2x 0.180069259 Present in Sprinter OBD154_013/OBD154_015_1x 0.050106528 Present in Sprinter OBD154_033/OBD154_035_1:4x 0.283703806 Present in Sprinter OBD154_037/OBD154_039_1:8x 0.523402567 Present in Sprinter OBD154_041/OBD154_043_1x 0.64299739 Present in Sprinter OBD154_045/OBD154_047_1x 0.180069259 Present in stayer OBD154_049/OBD154_051_1:4x 0.11992508 Present in Sprinter OBD154_053/OBD154_055_1:2x 0.597203758 Present in Sprinter OBD154_057/OBD154_059_1:2x 0.663949317 Present in Sprinter OBD154_061/OBD154_063_1x 0.663949317 Present in stayer OBD154_069/OBD154_071_1x 0.23718116 Present in Sprinter OBD154_073/OBD154_075_1x 0.125083174 Present in stayer OBD154_077/OBD154_079_1x 0.422463565 Present in Sprinter OBD154_085/OBD154_087_1:2x 0.038860637 Present in Sprinter OBD154_093/OBD154_095_1:2x 0.075142123 Present in Sprinter OBD154_097/OBD154_099_1x 0.523402567 Present in Sprinter OBD154_105/OBD154_107_1:2x 0.210490032 Present in Sprinter OBD154_109/OBD154_lll_1:2x 0.387940572 Present in stayer OBD154_113/OBD154_115_1:4x 0.523402567 Present in stayer OBD154_117/OBD154_119_1x 0.659282164 Present in Sprinter OBD154_121/OBD154_123_1x 0.659282164 Present in stayer OBD154_125/OBD154_127_1:2x 0.006313179 Present in Sprinter OBD154_133/OBD154_135_1:2x 0.32961205 Present in Sprinter OBD154_137/OBD154_139_1x 0.663949317 Present in stayer OBD154_141/OBD154_143_1x 0.180069259 Present in Sprinter OBD154_149/OBD154_151_1:2x 0.678620772 Present in stayer OBD154_153/OBD154_155_1:8x 0.523402567 Present in Sprinter OBD154_157/OBD154_159_1:2x 0.038860637 Present in stayer OBD154_161/OBD154_163_1:2x 0.422463565 Present in stayer OBD154_165/OBD154_167_1x 0.180069259 Present in Sprinter OBD154_169/OBD154_171_1:4x 0.283703806 Present in Sprinter OBD154_177/OBD154_179_1x 0.23718116 Present in Sprinter OBD154_185/OBD154_187_1x 0.64299739 Present in stayer OBD154_201/OBD154_203_1x 0.11992508 Present in stayer OBD154_205/OBD154_207_1:2x 0.125083174 Present in Sprinter OBD154_209/OBD154_211_1:2x 0.253032887 Present in Sprinter OBD154_213/OBD154_215_1:2x 0.180069259 Present in stayer OBD154_217/OBD154_219_1x 0.387940572 Present in Sprinter OBD154_229/OBD154_231_1x 0.054191604 Present in stayer OBD154_237/OBD154_239_1x 0.23718116 Present in Sprinter OBD154_245/OBD154_247_1x 0.050106528 Present in stayer Table 18 shows the informative markers from the equine study, which are preferably used to type horses.

TABLE 19 RANKING Relative (*Elite T. Body COMBINED Strength Athlete) Code Age Height (cm) Mass (kg) VO2max/kg 3 Lifts (kg) (kg/kg) *1 C29 27 186.5 67 74.5 210 3.13 *2 C49 29 172.4 60 73.8 255 4.25 *3 C6 27 182 70.5 71.7 245 3.48 *4 C10 30 185.5 75 65.5 240 3.20 *5 C66 21 190.7 76 64.6 335 4.41 *6 C69 44 171 66 63.3 280 4.24 *7 C27 28 176 57 62.4 250 4.39  8 C8 21 183.3 75 61.3 325 4.33  9 C23 43 189.5 77 60.2 240 3.12 10 C28 33 193 72.5 60.2 225 3.10 11 C15 25 183 77 59.6 350 4.55 12 C67 43 179.3 74 58.4 240 3.24 13 B86 33 181 77.5 57.65 325 4.19 14 C32 47 166.6 67 57.5 170 2.54 15 C24 18 183 81 56.2 335 4.14 16 C25 51 184 75 56.1 210 2.80 17 C4 21 174 73 55.4 245 3.36 18 C9 24 185.5 70.5 55.1 260 3.69 19 C14 40 179.5 70 54.7 280 4.00 20 A50 24 173.1 65 54.6 355 5.46 21 C60 24 180 77.5 54.6 335 4.32 22 C19 29 188 88 53.7 260 2.95 23 C35 43 173.3 68 51 200 2.94 24 A57 28 171.6 60 49.7 355 5.92 25 C12 48 175 92 49.5 295 3.21 26 B48 21 170.5 55 49.4 195 3.55 27 A21 30 188.5 80 48.9 415 5.19 28 B52 45 181.9 68.5 48.7 155 2.26 29 A20 37 168 69 48.4 465 6.74 30 A54 18 163 69 47.8 425 6.16 31 A31 25 181.2 78 47.1 465 5.96 32 A56 25 176.6 82.5 46.4 380 4.61 33 A55 18 163 67.5 45.7 435 6.44 34 A3 28 174 70 44.6 390 5.57 35 B70 28 172.4 63.5 44.4 200 3.15 36 A13 28 172 75 44 300 4.00 37 B63 49 181.6 90 42.9 170 1.89 38 A2 26 181 92.5 42.3 475 5.14 38 A36 20 189.2 92 42.1 540 5.87 40 A5 42 176 88 42 487.5 5.54 41 A41 27 175.3 79.5 41.8 475 5.97 42 A22 28 176 85 41 530 6.24 43 A59 27 184.8 80 39.3 400 5.00 44 A11 29 158 65.5 39.1 385 5.88 45 B46 44 180.6 75 39 270 3.60 46 B43 42 187.4 73 38.85 125 1.71 47 A30 24 183.5 81 37 530 6.54 48 B74 34 178.4 77.5 37 320 4.13 48 B44 44 170.9 77 36.9 190 2.47 50 A53 23 173 68 36.8 350 5.15 51 B78 27 188.2 98 36.5 250 2.55 52 A7 22 178 85 36 490 5.76 53 B77 45 169.1 88.5 35.9 300 3.39 54 B45 41 175.4 88.5 35.7 230 2.60 55 B68 42 176.5 88 35.5 275 3.13 56 B85 39 184.9 106 35.3 330 3.11 57 A58 23 175 70 35.1 350 5.00 58 B37 31 192.5 123 34.7 310 2.52 59 B62 33 199.6 109.5 34.5 280 2.56 60 B33 44 177.4 88.5 33.3 255 2.88 61 B75 22 178.5 99 33.2 330 3.33 62 B42 45 168.1 79 32.9 250 3.16 63 B79 54 179 71 32.6 140 1.97 64 B73 46 175.1 106.5 32.1 270 2.54 65 B64 36 181.5 89.5 32.1 285 3.18 66 B18 25 172.5 82 32 165 2.01 67 B82 35 170.3 88 32 315 3.58 68 B71 42 184 95 31.8 260 2.74 69 B16 41 174.5 79 31.1 260 3.29 70 B61 29 180.9 97.5 31 190 1.95 71 B65 33 181 65.5 31 145 2.21 72 B38 21 194.2 73.5 30.5 130 1.77 73 B83 43 186.7 94 30 290 3.09 74 B81 43 174.8 86.5 29.9 280 3.24 75 B80 47 185.6 85 29.9 170 2.00 76 B17 31 171.5 89.5 29.1 345 3.85 77 A1 29 176.5 89.5 28.1 467 5.22 78 B39 26 185 97 28 200 2.06 79 B87 34 187.1 101 27.9 235 2.33 80 B72 33 183.5 134.5 27.8 280 2.08 81 B26 30 197.5 131.5 27.1 275 2.09 82 B51 33 175.4 99 27 270 2.73 83 B34 25 175.5 92.5 25.9 300 3.24 84 B76 24 196.7 74 24.5 144.5 1.95 85 B40 34 169.8 78.5 24.3 170 2.17 KEY: RELATIVE STRENGTH (STRONG GROUP) = BLUE RELATIVE FITNESS (CARDIO GROUP) = ORANGE SEDENTARY (UNTRAINED GROUP) = GREEN *DIDN”T MEET CRITERIA (PERFORMANCE) = RED) GENETIC DISORDER = BLACK

TABLE 20 Relative T. Body COMBINED Strength RANKING Code Age Height (cm) Mass (kg) VO2max/kg 3 Lifts (kg) (kg/kg)  1 A20 37 168 69 48.4 465 6.74  2 A30 24 183.5 81 37 530 6.54  3 A55 18 163 67.5 45.7 435 6.44  4 A22 28 176 85 41 530 6.24  5 A54 18 163 69 47.8 425 6.16  6 A41 27 175.3 79.5 41.8 475 5.97  7 A31 25 181.2 78 47.1 465 5.96  8 A57 28 171.6 60 49.7 355 5.92 *9 A11 29 158 65.5 39.1 385 5.88 10 A36 20 189.2 92 42.1 540 5.87 11 A7 22 178 85 36 490 5.76 12 A3 28 174 70 44.6 390 5.57 13 A5 42 176 88 42 487.5 5.54 14 A50 24 173.1 65 54.6 355 5.46 15 A1 29 176.5 89.5 28.1 467 5.22 16 A21 30 188.5 80 48.9 415 5.19 17 A53 23 173 68 36.8 350 5.15 18 A2 26 181 92.5 42.3 475 5.14 19 A58 23 175 70 35.1 350 5.00 20 A59 27 184.8 80 39.3 400 5.00 21 A56 25 176.6 82.5 46.4 380 4.61 22 C15 25 183 77 59.6 350 4.55 23 C66 21 190.7 76 64.6 335 4.41 24 C27 28 176 57 62.4 250 4.39 25 C8 21 183.3 75 61.3 325 4.33 26 C60 24 180 77.5 54.6 335 4.32 27 C49 29 172.4 60 73.8 255 4.25 28 C69 44 171 66 63.3 280 4.24 29 B86 33 181 77.5 57.65 325 4.19 30 C24 18 183 81 56.2 335 4.14 31 B74 34 178.4 77.5 37 320 4.13 32 A13 28 172 75 44 300 4.00 33 C14 40 179.5 70 54.7 280 4.00 34 B17 31 171.5 89.5 29.1 345 3.85 35 C9 24 185.5 70.5 55.1 260 3.69 36 B46 44 180.6 75 39 270 3.60 37 B82 35 170.3 88 32 315 3.58 38 B48 21 170.5 55 49.4 195 3.55 38 C6 27 182 70.5 71.7 245 3.48 40 B77 45 169.1 88.5 35.9 300 3.39 41 C4 21 174 73 55.4 245 3.36 42 B75 22 178.5 99 33.2 330 3.33 43 B16 41 174.5 79 31.1 260 3.29 44 C67 43 179.3 74 58.4 240 3.24 45 B34 25 175.5 92.5 25.9 300 3.24 46 B81 43 174.8 86.5 29.9 280 3.24 47 C12 48 175 92 49.5 295 3.21 48 C10 30 185.5 75 65.5 240 3.20 48 B64 36 181.5 89.5 32.1 285 3.18 50 B42 45 168.1 79 32.9 250 3.16 51 B70 28 172.4 63.5 44.4 200 3.15 52 C29 27 186.5 67 74.5 210 3.13 53 B68 42 176.5 88 35.5 275 3.13 54 C23 43 189.5 77 60.2 240 3.12 55 B85 39 184.9 106 35.3 330 3.11 56 C28 33 193 72.5 60.2 225 3.10 57 B83 43 186.7 94 30 290 3.09 58 C19 29 188 88 53.7 260 2.95 59 C35 43 173.3 68 51 200 2.94 60 B33 44 177.4 88.5 33.3 255 2.88 61 C25 51 184 75 56.1 210 2.80 62 B71 42 184 95 31.8 260 2.74 63 B51 33 175.4 99 27 270 2.73 64 B45 41 175.4 88.5 35.7 230 2.60 65 B62 33 199.6 109.5 34.5 280 2.56 66 B78 27 188.2 98 36.5 250 2.55 67 C32 47 166.6 67 57.5 170 2.54 68 B73 46 175.1 106.5 32.1 270 2.54 69 B37 31 192.5 123 34.7 310 2.52 70 B44 44 170.9 77 36.9 190 2.47 71 B87 34 187.1 101 27.9 235 2.33 72 B52 45 181.9 68.5 48.7 155 2.26 73 B65 33 181 65.5 31 145 2.21 74 B40 34 169.8 78.5 24.3 170 2.17 75 B26 30 197.5 131.5 27.1 275 2.09 76 B72 33 183.5 134.5 27.8 280 2.08 77 B39 26 185 97 28 200 2.06 78 B18 25 172.5 82 32 165 2.01 79 B80 47 185.6 85 29.9 170 2.00 80 B79 54 179 71 32.6 140 1.97 81 B76 24 196.7 74 24.5 144.5 1.95 82 B61 29 180.9 97.5 31 190 1.95 83 B63 49 181.6 90 42.9 170 1.89 84 B38 21 194.2 73.5 30.5 130 1.77 85 B43 42 187.4 73 38.85 125 1.71 *REMOVE - HALLMANS SYNDROME KEY: RELATIVE STRENGTH (STRONG GROUP) = BLUE RELATIVE FITNESS (CARDIO GROUP) = ORANGE SEDENTARY (UNTRAINED GROUP) = GREEN DIDN'T MEET CRITERIA (PERFORMANCE) = RED) GENETIC DISORDER = BLACK

TABLE 21.a Gene Gene Name Function ACACB Acetyl-CoA Protein Coding gene. Biotin Deficiency. Diabetes Mellitus. Noninsulin- Carboxylase Beta Dependent. Associated with Metformin pathways. Pharmacodynamics and Regulation of cholestrol biosynthesis by SREBP. ACBD6 Acyl-CoA Binding Protein Coding gene. Related to Fatty-Acyl-CoA Biosynthesis and Domain Containing 6 Metabolism. ADRB3 Adrenoceptor Beta 3 Protein Coding gene. Body Mass Index Quantitative Trait Locus 11. Low Compliance Bladder. Related to Monoamine GPCRs and Peptide ligand- binding receptors pathways. ALDH1A2 Aldehyde Protein Coding Gene. Associated with Diaphragm Disease and Neural Tube Dehydrogenase 1 Defects. Family Member A2 ANO2 Anoctamin 2 Protein Coding Gene. Associated with Von Willebrand disease and Scrotal Carcinoma. Related to Olfactory Signaling Pathway and Ion channel transport. B3GAT1 Beta-1,3- Protein Coding Gene. Associated with Renal Adenoma and Malignant Glucuronyltransferase Glandular Tumor Of Peripheral Nerve Sheath. Related to 1 Glycosaminoglycan metabolism and Metabolism pathways. B3GAT2 Beta-1,3- Protein Coding gene. Diseases associated with B3GAT2 include Colonic Glucuronyltransferase Benign Neoplasm. Among its related pathways are Glycosaminoglycan 2 metabolism and Metabolism. Involved in the biosynthesis of L2/HNK-1 carbohydrate epitope on both glycolipids and glycoproteins. BMP7 Bone Morphogenetic Protein Coding gene. Diseases associated with BMP7 Protein 7 include Spondylolisthesis and Renal Fibrosis. Among its related pathways are Apoptotic Pathways in Synovial Fibroblasts and PEDF Induced Signaling. Induces cartilage and bone formation. May be the osteoinductive factor responsible for the phenomenon of epithelial osteogenesis. Plays a role in calcium regulation and bone homeostasis. C1GALT1 Core 1 Synthase, Protein Coding gene. Diseases associated with C1GALT1 include Iga Glycoprotein-N- Glomerulonephritis and Hypersensitivity Vasculitis. Among its related Acetylgalactosamine pathways are Ectoderm Differentiation and Metabolism of proteins. CALCR Calcitonin Receptor Protein Coding gene. Diseases associated with CALCR include Osteoporosis and Bone Mineral Density Quantitative Trait Locus 15. Among its related pathways are RANK Signaling in Osteoclasts and Osteoclast differentiation. CARD11 Caspase Recruitment Protein Coding gene. Diseases associated with CARD11 include B-Cell Domain Family Expansion With Nfkb And T-Cell Anergy and Immunodeficiency 11. Member 11 Involved in the costimulatory signal essential for T-cell receptor (TCR)- mediated T-cell activation. CASP9 Caspase 9 Protein Coding gene. Diseases associated with CASP9 include Brain Meningioma and Inflammatory Bowel Disease 7. Among its related pathways are Constitutive Signaling by AKT1 E17K in Cancer and Apoptotic Pathways in Synovial Fibroblasts. CBL Cbl Proto-Oncogene Protein Coding gene. Diseases associated with CBL include Noonan Syndrome-Like Disorder With Or Without Juvenile Myelomonocytic Leukemia and Juvenile Myelomonocytic Leukemia. Among its related pathways are Negative regulation of FGFR3 signaling and RANK Signaling in Osteoclasts. CD36 CD36 Molecule Protein Coding gene. Diseases associated with CD36 include Platelet Glycoprotein Iv Deficiency and Malaria. Among its related pathways are Cytokine Signaling in Immune system and Aryl Hydrocarbon Receptor. COL13A1 Collagen Type XIII Protein Coding gene. Diseases associated with COL13A1 Alpha 1 Chain include Myasthenic Syndrome, Congenital, 19and Postsynaptic Congenital Myasthenic Syndromes. Among its related pathways are Integrin Pathway and ERK Signaling. COL25A1 Collagen Type XXV Protein Coding gene. Diseases associated with COL25A1 include Fibrosis Of Alpha 1 Chain Extraocular Muscles, Congenital, 5 and Congenital Ptosis. Among its related pathways are Integrin Pathway and ERK Signaling. COL4A2 Collagen Type IV Protein Coding gene. Diseases associated with COL4A2 Alpha 2 Chain include Porencephaly 2 and Hemorrhage, Intracerebral. Among its related pathways are Integrin Pathway and ERK Signaling. COL5A1 Collagen Type V Protein Coding gene. Diseases associated with COL5A1 include Ehlers- Alpha 1 Chain Danlos Syndrome, Classic Type, 1and Ehlers-Danlos Syndrome Type 2. Among its related pathways are Integrin Pathway and ERK Signaling. CYGB Cytoglobin Protein Coding gene. Diseases associated with CYGB include Ancylostomiasis. Among its related pathways are Metabolism and eNOS activation and regulation. DGKH Diacylglycerol Kinase Protein Coding gene. Diseases associated with DGKH include Adrenal Eta Medulla Cancer and Extra-Adrenal Pheochromocytoma. Among its related pathways are Response to elevated platelet cytosolic Ca2+ and Signaling by GPCR. DIAPH3 Diaphanous Related Protein Coding gene. Diseases associated with DIAPH3 include Auditory Formin 3 Neuropathy, Autosomal Dominant, 1and Autosomal Dominant Non- Syndromic Sensorineural Deafness Type Dfna. Among its related pathways are Actin Nucleation by ARP-WASP Complex and G-protein signaling RhoB regulation pathway. DKK3 Dickkopf WNT Protein Coding gene. Diseases associated with DKK3 include Oral Signaling Pathway Submucous Fibrosis. Among its related pathways are CDK-mediated Inhibitor 3 phosphorylation and removal of Cdc6 and Regulation of Wnt/B-catenin Signaling by Small Molecule Compounds. DLK1 Delta Like Non- Protein Coding gene. Diseases associated with DLK1 include Temple Canonical Notch Syndrome and Idiopathic Central Precocious Puberty. Among its related Ligand 1 pathways are Signaling by NOTCH1 and NOTCH2 Activation and Transmission of Signal to the Nucleus. DOK5 Docking Protein 5 Protein Coding gene. Among its related pathways are Developmental Biology and Brain-Derived Neurotrophic Factor (BDNF) signaling pathway. EGR3 Early Growth Protein Coding gene. Diseases associated with EGR3 include Patella, Response 3 Chondromalacia Of and Ancylostomiasis. Among its related pathways are Circadian rythm related genes and Viral carcinogenesis. EHD1 EH Domain Protein Coding gene. Diseases associated with EHD1 include Venous Containing 1 Hemangioma and Photoallergic Dermatitis. Among its related pathways are Response to elevated platelet cytosolic Ca2+ and Angiopoietin Like Protein 8 Regulatory Pathway. EMCN Endomucin Protein Coding gene. mucin-like sialoglycoprotein that interferes with the assembly of focal adhesion complexes and inhibits interaction between cells and the extracellular matrix. ETS1 ETS Proto-Oncogene Protein Coding gene. Diseases associated with ETS1 include Jacobsen 1, Transcription Syndrome and Bone Ewing's Sarcoma. Among its related pathways Factor are Neural Crest Differentiation and ErbB signaling pathway. EYA1 EYA Transcriptional Protein Coding gene. Diseases associated with EYA1 Coactivator And include Otofaciocervical Syndrome 1and Branchiootorenal Syndrome 1. Phosphatase 1 Among its related pathways are DNA Double-Strand Break Repair and DNA Double Strand Break Response.

TABLE 21.b Gene Gene Name Function FBLN2 Fibdin 2 Protein Coding gene. Diseases associated with FBLN2 include Familial Osteochondritis Dissecans and Osteochondritis Dissecans. Among its related pathways are Cell adhesion_Cell-matrix glycoconjugates and Elastic fibre formation. FBXO32 F-Box Protein 32 Protein Coding gene. Diseases associated with FBXO32 include Muscle Hypertrophy and Muscle Tissue Disease. Among its related pathways are Innate Immune System and FoxO family signaling. FOXO1 Forkhead Box O1 Protein Coding gene. Diseases associated with FOXO1 include Rhabdomyosarcoma 2 and Rhabdomyosarcoma. Among its related pathways are Constitutive Signaling by AKT1 E17K in Cancer and Cytokine Signaling in Immune system. FOXO3 Forkhead Box O3 Protein Coding gene. Diseases associated with FOXO3 include Chromosome 6Q Deletion and Rhabdomyosarcoma. Among its related pathways are Constitutive Signaling by AKT1 E17K in Cancer and NFAT and Cardiac Hypertrophy. FTO FTO, Alpha- Protein Coding gene. Diseases associated with FTO include Growth Ketoglutarate Retardation, Developmental Delay, And Facial Dysmorphism and Body Mass Dependent Index Quantitative Trait Locus 14. Among its related pathways are DNA Dioxygenase Damage Reversaland FTO Obesity Variant Mechanism. GPC5 Glypican 5 Protein Coding gene. Diseases associated with GPC5 include Simpson-Golabi- Behmel Syndrome and Tetralogy Of Fallot. Among its related pathways are Glycosaminoglycan metabolism and CDK-mediated phosphorylation and removal of Cdc6. GPC6 Glypican 6 Protein Coding gene. Diseases associated with GPC6 include Omodysplasia 1 and Omodysplasia. Among its related pathways are Apoptotic Pathways in Synovial Fibroblasts and PAK Pathway. GRB10 Growth Factor Protein Coding gene. Diseases associated with GRB10 include Silver-Russell Receptor Bound Syndrome and Albright's Hereditary Osteodystrophy. Among its related Protein 10 pathways are Beta-Adrenergic Signaling and RET signaling. GSN Gelsolin Protein Coding gene. Diseases associated with GSN include Amyloidosis, Finnish Type and Lattice Corneal Dystrophy Type Ii. Among its related pathways are N-cadherin signaling events and Apoptosis and survival Caspase cascade. HDAC9 Histone Protein Coding gene. Diseases associated with HDAC9 include Gastrointestinal Deacetylase 9 Neuroendocrine Tumor and Cutaneous T Cell Lymphoma. Among its related pathways are PEDF Induced Signaling and Signaling by NOTCH1. HOXC6 Homeobox C6 Protein Coding gene. Gene Ontology (GO) annotations related to this gene include DNA binding transcription factor activity and transcription corepressor activity. IGF1R Insulin Like Growth Protein Coding gene. Diseases associated with IGF1R include Insulin-Like Factor 1 Receptor Growth Factor I and Ring Chromosome 15. Among its related pathways are Apoptotic Pathways in Synovial Fibroblasts and NFAT and Cardiac Hypertrophy. IL1RAP Interleukin 1 Protein Coding gene. Diseases associated with IL1RAP include Stromal Receptor Keratitis and Chromosome Xp21 Deletion Syndrome. Among its related Accessory Protein pathways are Bacterial infections in CF airways and IL-1 signaling pathway. KDM1A Lysine Protein Coding gene. Diseases associated with KDM1A include Cleft Palate, Demethylase 1A Psychomotor Retardation, And Distinctive Facial Features and Kbg Syndrome. Among its related pathways are Response to elevated platelet cytosolic Ca2+ and Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3. LAMA2 Laminin Subunit Protein Coding gene. Diseases associated with LAMA2 include Muscular Alpha 2 Dystrophy, Congenital Merosin-Deficient, 1Aand Congenital Muscular Dystrophy Type 1A. Among its related pathways are MET promotes cell motility and Integrin Pathway. LCK LCK Proto- Protein Coding gene. Diseases associated with LCK include Immunodeficiency Oncogene, Src 22 and Cd45 Deficiency. Among its related pathways are G-protein signaling N- Family Tyrosine RAS regulation pathway and Cytokine Signaling in Immune system. Kinase LDB2 UM Domain Protein Coding gene. Diseases associated with LDB2 include Retinal Binding 2 Detachment. Among its related pathways are Ectoderm Differentiation. LMO4 LIM Domain Only 4 Protein Coding gene. Diseases associated with LMO4 include Precursor T-Cell Acute Lymphoblastic Leukemia. Among its related pathways are IL-6 signaling pathway and Embryonic and Induced Pluripotent Stem Cell Differentiation Pathways and Lineage-specific Markers. MAPK10 Mitogen-Activated Protein Coding gene. Diseases associated with MAPK10 Protein Kinase 10 include Pertussis and Pneumococcal Meningitis. Among its related pathways are PEDF Induced Signaling and Toll-like receptor signaling pathway. MBNL1 Muscleblind Like Protein Coding gene. Diseases associated with MBNL1 include Myotonic Splicing Regulator Dystrophy and Myotonic Dystrophy 1. Among its related pathways 1 are Adipogenesis. MYBPC1 Myosin Binding Protein Coding gene. Diseases associated with MYBPC1 Protein C, Slow include Arthrogryposis, Distal, Type 1B and Lethal Congenital Contracture Type Syndrome 4. Among its related pathways are Cardiac conduction and Striated Muscle Contraction. MYH1 Myosin Heavy Protein Coding gene. Diseases associated with MYH1 include Retinitis Chain 1 Pigmentosa 67. Among its related pathways are PAK Pathway and ERK Signaling. MYO18B Myosin XVIIIB Protein Coding gene. Diseases associated with MYO18B include Klippel-Feil Syndrome 4, Autosomal Recessive, With Nemaline Myopathy And Facial Dysmorphism and Lung Large Cell Carcinoma. NCAM1 Neural Cell Protein Coding gene. Diseases associated with NCAM1 Adhesion Molecule include Rabies and Blastic Plasmacytoid Dendritic Cell. Among its related 1 pathways are RET signaling and Cytokine Signaling in Immune system. NECTIN2 Nectin Cell Protein Coding gene. Diseases associated with NECTIN2 include Herpes Adhesion Molecule Simplex and Ovarian Cystic Teratoma. Among its related pathways are PAK 2 Pathway and Innate Immune System. An important paralog of this gene is PVR. NFKB1 Nuclear Factor Protein Coding gene. Diseases associated with NFKB1 Kappa B Subunit 1 include Immunodeficiency, Common Variable, 12and Common Variable Immunodeficiency. Among its related pathways are RANK Signaling in Osteoclasts and PEDF Induced Signaling. NR4A1 Nuclear Receptor Protein Coding gene. Diseases associated with NR4A1 include Fetal Subfamily 4 Group Adenoma and Tracheal Cancer. Among its related pathways are Constitutive A Member 1 Signaling by AKT1 E17K in Cancer and Aldosterone synthesis and secretion. NRXN1 Neurexin 1 Protein Coding gene. Diseases associated with NRXN1 include Pitt-Hopkins- Like Syndrome 2 and Chromosome 2P16.3 Deletion Syndrome. Among its related pathways are Transmission across Chemical Synapses and Protein- protein interactions at synapses. NTRK2 Neurotrophic Protein Coding gene. Diseases associated with NTRK2 include Obesity, Receptor Tyrosine Hyperphagia, And Developmental Delay and Epileptic Encephalopathy, Early Kinase 2 Infantile, 58. Among its related pathways are Apoptotic Pathways in Synovial Fibroblasts and ERK Signaling. PAG1 Phosphoprotein Protein Coding gene. Among its related pathways are Innate Immune Membrane System and B cell receptor signaling pathway (KEGG). Anchor With Giycosphingohpid Microdomains

TABLE 21.c Gene Gene Name Function PCK1 Phosphoenolpyruvate Protein Coding gene. Diseases associated with PCK1 Carboxykinase 1 include Phosphoenolpyruvate Carboxykinase Deficiency, Cytosolic and Pepck 1 Deficiency. Among its related pathways are Estrogen Receptor Pathway and Glycosaminoglycan metabolism. PDK3 Pyruvate Protein Coding gene. Diseases associated with PDK3 include Charcot- Dehydrogenase Marie-Tooth Disease, X-Linked Dominant, 6 and X-Linked Charcot-Marie- Kinase 3 Tooth Disease. Among its related pathways are Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins, and Metabolism. PHTF2 Putative Protein Coding gene. An important paralog of this gene is PHTF1. May Homeodomain play a role in transcription regulation. Transcription Factor 2 PIK3C3 Phosphatidylinositol Protein Coding gene. Diseases associated with PIK3C3 3-Kinase Catalytic include Amyotrophic Lateral Sclerosis 1. Among its related pathways Subunit Type 3 are wtCFTR and deltaF508 traffic/Late endosome and Lysosome (norm and CF) and Delta508-CFTR traffic/Sorting endosome formation in CF. SMAD7 SMAD Family Protein Coding gene. Diseases associated with SMAD7 include Colorectal Member 7 Cancer 3 and Keloids. Among its related pathways are Immune response IFN gamma signaling pathway and TGF-beta Receptor Signaling STIM1 Stromal Interaction Protein Coding gene. Diseases associated with STIM1 include Myopathy, Molecule 1 Tubular Aggregate, 1 and Immunodeficiency 10. Among its related pathways are Cardiac conduction and Platelet homeostasis. STK39 Serine/Threonine Protein Coding gene. Diseases associated with STK39 include Epilepsy, Kinase 39 Familial Temporal Lobe, 4 and Renal Tubular Transport Disease. Among its related pathways are Diuretics Pathway, Pharmacodynamics and Sweet Taste Signaling. STXBP4 Syntaxin Binding Protein Coding gene. Among its related pathways are Angiopoietin Like Protein 4 Protein 8 Regulatory Pathway and Glucose/Energy Metabolism. SULF2 Sulfatase 2 Protein Coding gene. Diseases associated with SULF2 include Juvenile Astrocytoma. Gene Ontology (GO) annotations related to this gene include calcium ion binding and arylsulfatase activity. An important paralog of this gene is SULF1. SYK Spleen Associated Protein Coding gene. Diseases associated with SYK include Hantavirus Tyrosine Kinase Pulmonary Syndrome and Mycobacterium Abscessus. Among its related pathways are RANK Signaling in Osteoclasts and Role of phospholipids in phagocytosis. TBX21 T-Box 21 Protein Coding gene. Diseases associated with TBX21 include Asthma, Nasal Polyps, And Aspirin Intolerance and Genital Herpes. Among its related pathways are Th1 Differentiation Pathway and Th17 cell differentiation. TGFB2 Transforming Growth Protein Coding gene. Diseases associated with TGFB2 include Loeys-Dietz Factor Bets 2 Syndrome 4 and Holt-Oram Syndrome. Among its related pathways are Apoptotic Pathways in Synovial Fibroblasts and PAK Pathway. TGFBR2 Transforming Growth Protein Coding gene. Diseases associated with TGFBR2 include Loeys- Factor Beta Receptor Dietz Syndrome 2 and Colorectal Cancer, Hereditary Nonpolyposis, Type 2 6. Among its related pathways are PAK Pathway and Chronic myeloid leukemia. THADA THADA, Armadillo Protein Coding gene. Diseases associated with THADA include Adenoma. Repeat Containing THNSL2 Threonine Synthase Protein Coding gene. A similar enzyme in mouse can catalyze the Like 2 degradation of O-phospho-homoserine to a-ketobutyrate, phosphate, and ammonia. This protein also has phospho-lyase activity on both gamma and beta phosphorylated substrates. TLR2 Toll Like Receptor 2 Protein Coding gene. Diseases associated with TLR2 include Leprosy 3 and Colorectal Cancer. Among its related pathways are Bacterial infections in CF airways and Toll-like receptor signaling pathway. TNFRSF25 TNF Receptor Protein Coding gene. Diseases associated with TNFRSF25 Superfamily include Type 1 Diabetes Mellitus 18 and Type 1 Diabetes Mellitus Member 25 17. Among its related pathways are PEDF Induced Signaling and Apoptosis Modulation and Signaling.

TABLE 21.d Gene Gene Name Function TTN Titin Protein Coding gene. Diseases associated with TTN include Hereditary Myopathy With Early Respiratory Failure and Tibial Muscular Dystrophy, Tardive. Among its related pathways are Cardiac conduction and Response to elevated platelet cytosolic Ca2+. UACA Uveal Autoantigen Protein Coding gene. Diseases associated with UACA With Coiled-Coil include Panuveitis and Graves' Disease. An important paralog of this gene Domains And is RAI14. Ankyrin Repeats WASL Wiskott-Aldrich Protein Coding gene. Diseases associated with WASL include Wiskott-Aldrich Syndrome Like Syndrome and Vaccinia. Among its related pathways are Development EGFR signaling via small GTPases and PAK Pathway. ZEB1 Zinc Finger E-Box Protein Coding gene. Diseases associated with ZEB1 include Corneal Binding Homeobox Dystrophy, Fuchs Endothelial, 6and Corneal Dystrophy, Posterior 1 Polymorphous, 3. Among its related pathways are PAK Pathway and Cytokine Signaling in Immune system. ZFHX3 Zinc Finger Protein Coding gene. Diseases associated with ZFHX3 include Prostate Homeobox 3 Cancer and Atrial Fibrillation. Among its related pathways are Circadian rythm related genes and Signaling pathways regulating pluripotency of stem cells. AGT Angiotensinogen Protein Coding gene. Diseases associated with AGT include Renal Tubular Dysgenesis and Hypertension, Essential. Among its related pathways are Signaling events mediated by PRL and Peptide hormone metabolism. BMPR1B Bone Protein Coding gene. Diseases associated with BMPR1B Morphogenetic include Acromesomelic Dysplasia, Demirhan Type and Brachydactyly, Type Protein Receptor A1, D. Among its related pathways are Akt Signaling and Ovarian Infertility Type 1B Genes. HTR2A 5- Protein Coding gene. Diseases associated with HTR2A include Major Hydroxytryptamine Depressive Disorder and Obsessive-Compulsive Disorder. Among its related Receptor 2A pathways are Monoamine GPCRs and Peptide ligand-binding receptors. PPARA Peroxisome Protein Coding gene. Diseases associated with PPARA include Fatty Liver Prollferator Disease and Alcoholic Cardiomyopathy. Among its related pathways Activated Receptor are Estrogen Receptor Pathway and Organelle biogenesis and maintenance. Alpha SOS1 SOS Ras/Rac Protein Coding gene. Diseases associated with SOS1 include Noonan Guanine Syndrome 4 and Fibromatosis, Gingival, 1. Among its related pathways are G- Nucleotide protein signaling N-RAS regulation pathway and RET signaling. Exchange Factor 1 SVEP1 Sushi, Von Protein Coding gene. Related to calcium ion binding and chromatin binding. Willebrand Factor Type A, EGF And Pentraxin Domain Containing 1 UBE3A Ubiquitin Protein Protein Coding gene. Diseases associated with UBE3A include Angelman Ligase E3A Syndrome and Angelman Syndrome Due To A Point Mutation. Among its related pathways are PI3K-Akt signaling pathway and Innate Immune System. HADHA Hydroxyacyl-CoA Protein Coding gene. Diseases associated with HADHA include Long-Chain 3- Dehyrdogenase Hydroxyacyl-Coa Dehydrogenase Deficiency and Mitochondrial Trifunctionai Trifunctional Protein Deficiency. Among its related pathways are Glycerophospholipid Multienzyme biosynthesis and Mitochondrial Fatty Acid Beta-Oxidation. Complex Subunit Alpha MTFR1 Mitochondrial Protein Coding gene. May play a role in mitochondrial aerobic respiration, Fission Regulator 1 organisation and fission. Chicken homolog promotes mitochondrial fission and mouse homolog protects cells from oxadative stress. MYL1 Myosin Light Chain Protein Coding gene. Among its related pathways are Cardiac 1 conduction and PAK Pathway. Related to calcium ion binding and structural constituent of muscle. MYOD1 Myogenic Protein Coding gene. Diseases associated with MYOD1 include Pleomorphic Differentiation 1 Rhabdomyosarcoma and Spindle Cell Rhabdomyosarcoma. Among its related pathways are Development NOTCHl-mediated pathway for NF-KB activity modulation and miRs in Muscle Cell Differentiation. NECTIN3 Nectin Cell Protein Coding gene. Among its related pathways are PAK Pathway and T Cell Adhesion Molecule Co-Signaling Pathway: Ligand-Receptor Interactions. Plays a role in ocular 3 development involving the ciliary body. Mutations are believed to result in congenital ocular defects. PON1 Paraoxonase 1 Protein Coding gene. Diseases associated with PON1 include Microvascular Complications Of Diabetes 5 and Amyotrophic Lateral Sclerosis 1. Among its related pathways are Metabolism and Arachidonic acid metabolism. Polymorphisms in the gene may be associated with coronary heart disease and diabetic retinopathy. COL1A2 Collagen Type 1 rotein Coding gene. Diseases associated with COL1A2 include Osteogenesis Alpha 2 Chain Imperfecta, Type Iii and Type Iv, atypical Marfan syndrome, Ehlers-Danos syndrome type VIIB and recessive Ehlers-Danos syndrome. Among its related pathways are Cytokine Signaling in Immune system and Integrin Pathway. COX6A1 Cytochrome C Protein Coding gene. Diseases associated with COX6A1 include Charcot- Oxidase Subunit Marie-Tooth Disease, Recessive Intermediate D and Charcot-Marie-Tooth 6A1 Disease, Axonal, Type 2R. Among its related pathways are Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins, and Gene Expression. GGPS1 Geranylgeranyl Protein Coding gene. Diseases associated with GGPS1 include Osteogenesis Diphosphate Imperfecta, Type V. Among its related pathways are Regulation of cholesterol Synthase 1 biosynthesis by SREBP (SREBF) and Terpenoid backbone biosynthesis. MUSK Muscle Associated Protein Coding gene. Diseases associated with MUSK include Myasthenic Receptor Tyrosine Syndrome, Congenital, 9, Associated With Acetylcholine Receptor Kinase Deficiency and Fetal Akinesia Deformation Sequence. Among its related pathways are ERK Signaling and ECM proteoglycans. MYOT Myotilin Protein Coding gene. Diseases associated with MYOT include Myopathy, Myofibrillar, 3 and Muscular Dystrophy, Limb-Girdle, Type 1A. PPP1R9A Protein Protein Coding gene. Diseases associated with PPP1R9A Phosphatase 1 include Hepatosplenic T-Cell Lymphoma. Among its related pathways Regulatory Subunit are Beta-Adrenergic Signaling and Activation of cAMP-Dependent PKA. Also 9A related to actin binding and cytoiskeleton reorganisation. RB1 RB Transcriptional Protein Coding gene. Diseases associated with RB1 Corepressor 1 include Retinoblastoma and Bladder Cancer. Among its related pathways are Mitotic Prophase and Chronic myeloid leukemia. SLC25A13 Solute Carrier Protein Coding gene. Diseases associated with SLC25A13 Family 25 Member include Citrullinemla, Type Ii, Neonatal-Onset and Citrullinemia, Type Ii, 13 Adult-Onset. Among its related pathways are Glycosaminoglycan metabolism and Metabolism. ACE2 Angiotensin 1 Protein Coding gene. Diseases associated with ACE2 include Severe Acute Converting Enzyme Respiratory Syndrome and Neurogenic Hypertension. Among its related 2 pathways are Peptide hormone metabolism and Collagen chain trimerization. May play a role in the regulation of cardiovasuclar and renal function and fertility. DNAH5 Dynein Axonemal Protein Coding gene. Diseases associated with DNAH5 include Ciliary Heavy Chain 5 Dyskinesia, Primary, 3, Primary Ciliary Dyskinesia and Kartagener syndrome. Among its related pathways are Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins. ITGAV Integrin Subunit Protein Coding gene. Diseases associated with ITGAV include West Nile Alpha V Virus and Cerebral Hypoxia. Among its related pathways are VEGF Signaling Pathway and Primary Focal Segmental Glomerulosclerosis FSGS. Protein may regulate angiogenesis and cancer progression. MSTN Myostatin Protein Coding gene. Diseases associated with MSTN include Muscle Hypertrophy and Myostatin-Related Muscle Hypertrophy. Among its related pathways are Hypertrophy Model and Factors and pathways affecting insulin- like growth factor (IGF1)-Akt signaling. SOCS7 Suppressor Of Protein Coding gene. Among its related pathways are Jak-STAT Cytokine signaling pathway (KEGG) and Jak/STAT Signaling Pathway Signaling 7 Intracellular Regulation. Functions in insulin signaling and glucose homeostasis. SRI Sorcin Protein Coding gene. Regulates intracellular calcium homeostasis. Diseases associated with SRI include Interstitial Myocarditis and Apical Myocardial Infarction. Among its related pathways are Cardiac conduction and Response to elevated platelet cytosolic Ca2+.

Training type Marker Training Odds Ratio Combined Cardio Strength OBD142_029.031_1x Present in Endurance and Strength 7.2 0.016681 0.06669 0.01613 OBD142_061.063_1.8x Present in Endurance and Strength 8.2 0.0185106 0.11741 0.1068 OBD142_069.071_1.2x Present in Endurance and Strength 8 0.0025561 0.06669 0.05767 OBD142_089.091_1x Present in Endurance and Strength 2.9 0.1237527 0.40123 0.1806 OBD142_137.139_1.2x Present in Endurance and Strength 8 0.0627014 0.11741 0.18262 OBD142_081.083_1.4x Present in Endurance 6 0.1392395 0.07048 0.79999 OBD142_189.191_1x Present in Endurance 4.5 0.1196946 0.11741 0.84529 OBD142_213.215_1.4x Present in Endurance 2.25 1 0.69409 0.13523 OBD142_017.019_1.2x Present in Strength 4 0.7249505 0.54542 0.28124 OBD142_037.039_1x Present in Strength 12 0.1525177 1 0.02526 OBD142_065.067_1x Present in Strength 5 0.131911 0.54542 0.05767 OBD142_133.135_1x Present in Strength 4 0.4615609 1 0.01613 OBD142_253.255_1.2x Present in Strength 12 0.4496075 0.6101 0.02421 OBD142_353.355_1x Present in Strength 9 0.1196946 1 0.01615 OBD142_477.479_1x Present in Strength 9 0.4275177 1 0.02526 OBD142_181.183_1.4x Present in Strength 2 0.7559581 0.74071 0.17781 OBD142_397.399_1x Present in Strength 2 0.1516371 0.66843 0.09668 Table 22 shows preferred markers from the equine study and the traits they relate to, which are preferably used to type horses.

PCR Marker Phenotype OBD154_125/OBD154_127 Sprinter OBD154_085/OBD154_087 Sprinter OBD154_157/OBD154_159 Stayer OBD154_013/OBD154_015 Sprinter OBD154_245/OBD154_247 Sprinter OBD154_229/OBD154_231 Sprinter OBD154_093/OBD154_095 Sprinter OBD154_049/OBD154_051 Sprinter OBD154_201/OBD154_203 Stayer OBD154_041/OBD154_043 Stayer OBD154_073/OBD154_075 Stayer OBD154_205/OBD154_207 Sprinter OBD154_009/OBD154_011 Sprinter OBD154_045/OBD154_047 Stayer OBD154_141/OBD154_143 Sprinter OBD154_165/OBD154_167 Sprinter OBD154_213/OBD154_215 Stayer Table 23 shows preferred markers from the equine study and the traits they relate to, which are preferably used to type horses.

TABLE 24.a No. Probe GeneLocus 1 ORF2_1_133335365_133342248_133252663_133254033_RR ORF2 2 ORF17_21_46168522_46170441_46128519_46131714_FR ORF17 3 ORF37_7_80905043_80905799_80946828_80948039_FF ORF37 4 ORF5_22_44079168_44079873_44099430_44101885_RR ORF5 5 ORF33_23_51893485_51894717_51879777_51881452_RR ORF33 6 ORF24_7_26919921_26921163_26962320_26963327_RF ORF24 7 ORF1_3_38982976_38984987_38897821_38902754_RR ORF1 8 ORF39_3_37427338_37427846_37369331_37372145_FF ORF39 9 ORF21_27_18057476_18059723_18216584_18221307_FF ORF21 10 ORF9_9_19477415_19483037_19371208_19377216_RF ORF9 11 ORF11_25_15754740_15756330_15827853_15831235_FR ORF11 12 ORF41_2_44125472_44130831_44114366_44115500_FR ORF41 13 ORF12_28_42033251_42034839_42111316_42112829_FR ORF12 14 ORF42_14_38556059_38561196_38515585_38519701_RR ORF42 15 ORF31_24_18025107_18025879_18089550_18090204_FR ORF31 16 ORF28_19_27971050_27974189_28029396_28030610_FR ORF28 17 ORF3_3_39072647_39081470_38902754_38905559_RR ORF3 18 ORF87_4_38678592_38682251_38712668_38720224_RF ORF87 19 ORF95_2_30297289_30298973_30249858_30251319_RF ORF95 20 ORF72_5_76755446_76755869_76713081_76716746_FR ORF72 21 ORF44_8_11915509_11916086_11887773_11890590_RR ORF44 22 ORF90_5_9229073_9235994_9247952_9249817_FR ORF90 23 ORF51_4_788561_790967_729450_732106_FR ORF51 24 ORF67_15_69928382_69930519_69848008_69851513_FF ORF67 25 ORF109_1_110780529_110783525_110809348_110820887_FF ORF109 26 ORF99_11_29755642_29761616_29820061_29826391_RR ORF99 27 ORF46_27_7694409_7697820_7673458_7673882_FR ORF46 28 ORF107_15_17634193_17641147_17623423_17624089_FR ORF107 29 ORF86_19_45858761_45861211_45775880_45782396_RR ORF86 30 ORF71_5_76755446_76755869_76727262_76728348_FF ORF71 31 ORF62_17_64192230_64193405_64341970_64343229_FF ORF62 32 ORF69_1_104390566_104392857_104321461_104322189_RF ORF69 33 ORF76_7_85946864_85949922_85987651_85988101_FR ORF76 34 ORF79_23_5314583_5315708_5202402_5204544_FR ORF79 35 ORF64_25_24906776_24910177_25031046_25032151_FF ORF64 36 ORF85_X_18614272_18616544_18648509_18649030_FR ORF85 37 ORF58_22_41701255_41702998_41789282_41790782_RF ORF58 38 ORF81_22_44079168_44079873_44118479_44121814_RR ORF81 39 ORF84_X_18614272_18616544_18641258_18647069_FR ORF84 40 ORF73_16_84538528_84540820_84582113_84585716_FR ORF73 41 ORF106_15_55284305_55291596_55156691_55157175_FF ORF106 42 ORF88_3_100800337_100801373_100744664_100751637_FF ORF88 [Table 24 shows markers identified in the equine study, which are preferably used to type horses.]

TABLE 24.b Probe sequence No. 60 mer 1 TTTAAAACTAAGTCTAACCGCCTGAAAGTCGAGAGGGAAGTGCTACGCATCCCGCGCACA 2 AGAGGCTCAAAACTTCTGTCTGGTAAATTCGATTTTCTCCTATTGCTCTACATCACTCGG 3 CCCCATAGGAGGCTTCTGGGAAGCCCAGTCGAGATGCATCCATGTTGTCATGGGTATAAG 4 TTCCTACCACCCAAATTCTATTATTCTATCGAGAGGCACCAGGATGCTGAGAGGATGAGA 5 TCGTGTTAGTTAAATCGGCCGATTTGTCTCGAGAAAAGAGAAGGACTGGGTCATGGTGGG 6 CCGCCTCGCCACAGCTCTCCAGTGAGATTCGATCCTTTTAAACTTTGTTAGGCAAGACCA 7 TTGATCTTTTTTAAAATAGGGATGGGGTTCGAGAGAAGGAGAATGAAGCAGAAAGCTTGT 8 CTGTAACCAGAGGAGCAGAGTCTGCACATCGATTCCTCTTACTGCACTGCAGGTCCAGGG 9 ACCCAAAATTTACTTGCAATCACTTTAATCGAGCTCTTGGATGTCTGGGGATTGTTCTGC 10 GATAGAATTAAACATTGAAGGCAAACTTTCGATTAGGGTTTTAGTTTTCTTTAAGTTTTT 11 GAGCACAGGTGCTGGATTCAGGCTTCCTTCGATTCAAACTTCCCTCACACTGACATTTTT 12 GGAGAAAAAGGGGCTTTACGCAGTCCATTCGATGCAGTCAGGAGTCAGGACAGCATCTCC 13 CACAATGCCTTCCCCTCTTCCACCCCTTTCGATCACTGTCCTTCGTACACTCAAGATATA 14 GTAAAAACCAGCTTCCAGGGACCAGATGTCGAGATCAGTATTGAAATGCACCATTTCATT 15 CATAAGAGATGACTGGCCTTTTGCTGTTTCGATGGCCCGGCTTCCTCTTTGGGACTTCAG 16 TAATGAAATTGTCTTTTTGTGTCTTTCTTCGAGGATTTCTAGACTTTCTGTGCATCACTA 17 AAGCATAAATTCGTTTTCCCCTTGACTTTCGAGACTCCATAAAGCACACGCACAAAGGCC 18 GTAACATGCTGAATAACAACATTTCAGTTCGAGCGTTGTGGCAGAGCTTCCTTGTTACTG 19 ACAGTGCTGCCTCTTCTGTGCAGATGCTTCGAAACCCATGTAATTTCATAGCTATGATGG 20 TTGCCTCCATTTTAAAATTGAAGAAACTTCGAATAAAATTGAAACATCCTACCACCAACA 21 CAGCTGGAGCTCAGCCGGATGCGCAACTTCGAGAAGAGATATTTGCACATCCGTGTTCGT 22 AGTGGGCCACCACTGCCTAAGAACTACTTCGAGGCCAATACTACTGTCGGCCGCATCCGT 23 GCCGTCGGTGGAGAAATTTAAAACTATTTCGAGTCAGTAACTGGACTCAGTTAAGGAAGG 24 CACTGAGCTGCACGAAGATGCTGCCATCGATTCTCAATTGGGAAAAGCACATGGGATATG 25 TTAAAAGTAAAGTAAGTAGAGGTCAGTCTCGAAGCTTTGAAGATTAGTTTTTGAACAGTG 26 CAAGAATCAGTTCTGAGAAATCAATGCCTCGAGAACCAACGAAACACTGGGCCGCCTGCA 27 TGAACATTATCCAGGAGCTCATACTGCTTCGATGACCACAGAGGCGCCAGAAGGCCACAG 28 CAATGTACAATCTACCAGGAACTGAAGTTCGAGCAGCACTTGGCTTTCTTCCTTTTTAGA 29 GAAAGCTGGGTATGGGAGTGTGCACACTTCGAGATCTCAGAAAGGGCATAACTGTATTTT 30 ATTGCCTCCATTTTAAAATTGAAGAAACTCGATGGAGTTTGGGTTTAAGCACTGCTTTTT 31 AGGCCTCGCCTATGAATAGCATACCAGCTCGATTATTCTTCTCTCACACAATTTCTGAAG 32 CTCCGCCCGCCAGCTCTGCAGCTTCCCTTCGACGCTTCCTACTTTTCTCCAGGAAATTAT 33 TCACTCCAGGACCCCCCCAGCCCTGTGTTCGAGGTTGTTTTGCCAGTCGTCTGTTTGGCA 34 GGAAACACAAAGTTCTTGGCAAAGCTTCGAGTCTTGGAGGTGTTGTTATTTGCCCAAAGC 35 GTGGCCTTATTTTGCAAAGGGGCAAACTTCGAAGGTGATGAAACGGAGGCCCAGAGAGGG 36 TACCTCCAGTCTTGGTTATTCTGAGAGTTCGAGTCAGGATTCAGACCCAAGTCTAACTCT 37 GGGTCCAAACCTGCAAATCCCCAGCTGTTCGAAAATGTGTCTGCTTTTTCATGGACACCA 38 TTCCTACCACCCAAATTCTATTATTCTATCGAGAGGCTGAGATGAACAAGGCAGACGCAG 39 TACCTCCAGTCTTGGTTATTCTGAGAGTTCGACAAGTGCGCTAGTGCCGCTTGTCAAGAG 40 ATAAATTCCTTTGTGAATTTTGATCTCTTCGAAGACTTGTTCTGTTGGAGGCATGTCCCT 41 CTTCCCCAAGAATTTTGGATTATATCTCTCGAGAAAGGGTAAGGAAGAGTCAAAGCTGTA 42 CAATTTCTGGGGATACAGTAGTGAAGAGTCGATGGCATGGGATCTCTGCTATTTATCTCT

TABLE 24.c Probe Location 4 kb Sequence Location No. Chr Start1 End1 Start2 End2 Chr Start1 1 1 133335365 133335396 133252663 133252694 1 133335365 2 21 46170410 46170441 46128519 46128550 21 46166440 3 7 80905768 80905799 80948008 80948039 7 80901798 4 22 44079168 44079199 44099430 44099461 22 44079168 5 23 51893485 51893516 51879777 51879808 23 51893485 6 7 26919921 26919952 26963296 26963327 7 26919921 7 3 38982976 38983007 38897821 38897852 3 38982976 8 3 37427815 37427846 37372114 37372145 3 37423845 9 27 18059692 18059723 18221276 18221307 27 18055722 10 9 19477415 19477446 19377185 19377216 9 19477415 11 25 15756299 15756330 15827853 15827884 25 15752329 12 2 44130800 44130831 44114366 44114397 2 44126830 13 28 42034808 42034839 42111316 42111347 28 42030838 14 14 38556059 38556090 38515585 38515616 14 38556059 15 24 18025848 18025879 18089550 18089581 24 18021878 16 19 27974158 27974189 28029396 28029427 19 27970188 17 3 39072647 39072678 38902754 38902785 3 39072647 18 4 38678592 38678623 38720193 38720224 4 38678592 19 2 30297289 30297320 30251288 30251319 2 30297289 20 5 76755838 76755869 76713081 76713112 5 76751868 21 8 11915509 11915540 11887773 11887804 8 11915509 22 5 9235963 9235994 9247952 9247983 5 9231993 23 4 790936 790967 729450 729481 4 786966 24 15 69930488 69930519 69851482 69851513 15 69926518 25 1 110783494 110783525 110820856 110820887 1 110779524 26 11 29755642 29755673 29820061 29820092 11 29755642 27 27 7697789 7697820 7673458 7673489 27 7693819 28 15 17641116 17641147 17623423 17623454 15 17637146 29 19 45858761 45858792 45775880 45775911 19 45858761 30 5 76755838 76755869 76728317 76728348 5 76751868 31 17 64193374 64193405 64343198 64343229 17 64189404 32 1 104390566 104390597 104322158 104322189 1 104390566 33 7 85949891 85949922 85987651 85987682 7 85945921 34 23 5315677 5315708 5202402 5202433 23 5311707 35 25 24910146 24910177 25032120 25032151 25 24906176 36 X 18616513 18616544 18648509 18648540 X 18612543 37 22 41701255 41701286 41790751 41790782 22 41701255 38 22 44079168 44079199 44118479 44118510 22 44079168 39 X 18616513 18616544 18641258 18641289 X 18612543 40 16 84540789 84540820 84582113 84582144 16 84536819 41 15 55291565 55291596 55157144 55157175 15 55287595 42 3 100801342 100801373 100751606 100751637 3 100797372

TABLE 24.d 4 kb Sequence Location No. End1 Start2 End2 PCR−Primer1_ID PCR_Primer1 1 133339366 133252663 133256664 OBD154_001 GGTATTGGAACTTCAGAGAGGTAGGC 2 46170441 46128519 46132520 OBD154_009 GAGGAGGGAGAGTGCTACTTGCC 3 80905799 80944038 80948039 OBD154_013 GCCCCATTGAGCATCACAGAGGG 4 44083169 44099430 44103431 OBD154_033 TCCCCACTTCTCCTCCACAAGGC 5 51897486 51879777 51883778 OBD154_037 CCCCAGGAGTGATGGCTCAGAAT 6 26923922 26959326 26963327 OBD154_041 GCCTCCCAAACCATTCCCTCGGA 7 38986977 38897821 38901822 OBD154_045 GCCCCATACACTGCTCACTGGCT 8 37427846 37368144 37372145 OBD154_049 CACTCCTGCCGCTGAGATTCCTG 9 18059723 18217306 18221307 OBD154_053 CCGCCATTGGGTTGTTTTGCCCC 10 19481416 19373215 19377216 OBD154_057 GCCTTGAGCATACCCACTGTCAG 11 15756330 15827853 15831854 OBD154_061 ACCAAGCACAGTGGCTGACACATCTG 12 44130831 44114366 44118367 OBD154_069 AAGCCCTGGAGTGGGAGATTGCT 13 42034839 42111316 42115317 OBD154_073 CAACCTGGAGTCCTGAAGACCCC 14 38560060 38515585 38519586 OBD154_077 CCACCTTGGCAAATGGCTTCTCTGCT 15 18025879 18089550 18093551 OBD154_085 CTCCCTGCCCTCCATTTGCCTTT 16 27974189 28029396 28033397 OBD154_093 GCACTGAGTTGTGGGTTTTCAAAGGT 17 39076648 38902754 38906755 OBD154_097 GCTATTTGCGTGGTGGTGACAATGAT 18 38682593 38716223 38720224 OBD154_105 ATCATCACCTTAGTATCCCCACCTCT 19 30301290 30247318 30251319 OBD154_109 AAGTGTCAGCCTCTGCCCGTAGC 20 76755869 76713081 76717082 OBD154_113 GGGTGAGGTTCTTTCCCTGTAGG 21 11919510 11887773 11891774 OBD154_117 GTCTCTTCTTCTCTCTGGTCGGC 22 9235994 9247952 9251953 OBD154_121 CCCACACCTCCAGTTGTCCCACA 23 790967 729450 733451 OBD154_125 TACTCTTCAAAAGCACAGCCAACGGG 24 69930519 69847512 69851513 OBD154_133 GGTGGAAGTCGTCTGCCAAGATG 25 110783525 110816886 110820887 OBD154_137 TGGCTAACTGTCTCCTCAAAATCCTA 26 29759643 29820061 29824062 OBD154_141 CGTAACACCCGAATCAGTGGAAGGAA 27 7697820 7673458 7677459 OBD154_149 GCCTCCTCTCCCTATCTCTGGAT 28 17641147 17623423 17627424 OBD154_153 CAGATGCTGGGTTTTGCCCTCAGG 29 45862762 45775880 45779881 OBD154_157 TGACTCTGCTGTAGATGTCCTGGCTC 30 76755869 76724347 76728348 OBD154_161 GGGTGAGGTTCTTTCCCTGTAGG 31 64193405 64339228 64343229 OBD154_165 GGTAGAAAGCGTTTAGCCCTGTATTT 32 104394567 104318188 104322189 OBD154_169 CACCTTCATCCTTCACCAAGTCCTGC 33 85949922 85987651 85991652 OBD154_177 CCCTCAACCCATTTCCTTCACTTGCC 34 5315708 5202402 5206403 OBD154_185 TGAGGATGGTCAGTGAGACTCGTAAA 35 24910177 25028150 25032151 OBD154_201 ACAGTAGACAGACAGCACAGGGTTTA 36 18616544 18648509 18652510 OBD154_205 AAAGGTGGTGGGCAGGACTCCAG 37 41705256 41786781 41790782 OBD154_209 ATGTAGGGCATCACCACAGCGTG 38 44083169 44118479 44122480 OBD154_213 TCCCCACTTCTCCTCCACAAGGC 39 18616544 18641258 18645259 OBD154_217 AAAGGTGGTGGGCAGGACTCCAG 40 84540820 84582113 84586114 OBD154_229 ACTCGGCTAACCCTCTACTTCAAGGT 41 55291596 55153174 55157175 OBD154_237 GGCGGCTGTGTGAGTTTTGCCAA 42 100801373 100747636 100751637 OBD154_245 ACCATTAGTTGGCTCATCTCCTTGCC

TABLE 24.e No. PCR-Primer2_ID PCR_Primer2 GLMNET 1 OBD154_003 GGAGGCAAGGCTGTGATGAAAGTCAA 0.044648292 2 OBD154_011 GTGAGTGGGTTTCCCTGCTGAAC 0.077266514 3 OBD154_015 GCTGCTGTGGGTTTCTGCGACAT 0.10805769 4 OBD154_035 GCCTGGAACAGTTGAGCAAACGC 0.052504077 5 OBD154_039 CCAGTGCCTCTCTTCAGCATCCC 0.016550856 6 OBD154_043 CTCACACAGAGAGGAGGAGAGGA 0.033835679 7 OBD154_047 CCCCAGGTTTGGAAGTTCTCAGC −0.031914355 8 OBD154_051 CGGAGCAGAACATTCGCCTAAGC 0.073432502 9 OBD154_055 GCAGTGTGACAAGGAAGCAGCAG 0.034421206 10 OBD154_059 ACCCTCAGAAATCCCTCCCAGGC 0.014137586 11 OBD154_063 TCTTCACCATTTTCTTGAGCACTGTG −0.034009396 12 OBD154_071 GCCAGCCACTGTCCCAAGGAGAT 0.046480779 13 OBD154_075 CGCAGGGCTAATCTTCCTCAACC −0.092997789 14 OBD154_079 TTTTGAGGGAGAGTCCGTGAAGC 0.018460556 15 OBD154_087 ATCACGGACAGGCACCTACGGCT 0.105247988 16 OBD154_095 ATCAAACTCCAGCAATCTGACTCCAG 0.067222042 17 OBD154_099 GCCAGGCTCACTCCTTTCCCTTTTAG 0.069540888 18 OBD154_107 GCCCTGAGACAAGCATTTTCCTCGTC 0.072250245 19 OBD154_111 CGGAGTCTCGTCCCGACATTTAC −0.021487184 20 OBD154_115 ACTGTGTGGGAGGAAGGTGGAGG −0.089547447 21 OBD154_119 CACCCACCTTTGTTCACCCGCTC 0.053341863 22 OBD154_123 CCCAGGTAGTCGTGGAAACGGAT −0.009481999 23 OBD154_127 CCCCTGGCTTTAGGCTTAGATTCTCT 0.184254198 24 OBD154_135 TTCTCGCCTGCTTCCTGCCTGTG 0.013549498 25 OBD154_139 GCCATTCGGTGACATCAGGGTGA −0.029260042 26 OBD154_143 AGAGTCACGGTTTCTGCCTATCAAGA 0.040466078 27 OBD154_151 CCTCTCGCTGAAGTCCCTGCCAT −0.026044566 28 OBD154_155 CAGGGAAGGGAGAATAGTCAGGG 0.05560739 29 OBD154_159 GGAGAGAAGATAGGCTGGCAATAGAT −0.111847127 30 OBD154_163 CACCTCCTCCCTCAACCCCTAAG −0.011075719 31 OBD154_167 ATTTAGGCACTTGGGAGAGGAGAGCC 0.052703232 32 OBD154_171 CTGATGATAGTTAGGGAGAGGTGAGT 0.072817076 33 OBD154_179 AAGGTTTGTGGCTCTTGAACATACCA 0.023527 34 OBD154_187 AATGGCACATCCTCCAACCCCAAACC −0.028512982 35 OBD154_203 TGTGTGTCTACTGCCAACTCTGCCCT −0.076839662 36 OBD154_207 CCTCAGGTCAGGTTTTGTCACGG 0.101263033 37 OBD154_211 CCGCCCGCATTGGCATCCGAATA 0.048686754 38 OBD154_215 CCGAGCCTTCTCCCTTTTCTCCA −0.060839024 39 OBD154_219 CAGAACTCCTCAGGCTCAGACAC 0.01900231 40 OBD154_231 CTGGCTCAATAAGAGTGCTTTCCTTG 0.10786072 41 OBD154_239 TGGCAGGGAAAGACTCGGAGGTC −0.04345676 42 OBD154_247 CCTCTTCCCTAACTGCGAAACAAAAC 0.059641358

TABLE 24.f No. Marker GLMNET 1 OBD154_001/OBD154_003_1:2x 0.044648292 2 OBD154_009/OBD154_011_1:2x 0.077266514 3 OBD154_013/OBD154_015_1x 0.10805769 4 OBD154_033/OBD154_035_1:4x 0.052504077 5 OBD154_037/OBD154_039_1:8x 0.016550856 6 OBD154_041/OBD154_043_1x 0.033835679 7 OBD154_045/OBD154_047_1x −0.031914355 8 OBD154_049/OBD154_051_1:4x 0.073432502 9 OBD154_053/OBD154_055_1:2x 0.034421206 10 OBD154_057/OBD154_059_1:2x 0.014137586 11 OBD154_061/OBD154_063_1x −0.034009396 12 OBD154_069/OBD154_071_1x 0.046480779 13 OBD154_073/OBD154_075_1x −0.092997789 14 OBD154_077/OBD154_079_1x 0.018460556 15 OBD154_085/OBD154_087_1:2x 0.105247988 16 OBD154_093/OBD154_095_1:2x 0.067222042 17 OBD154_097/OBD154_099_1x 0.069540888 18 OBD154_105/OBD154_107_1:2x 0.072250245 19 OBD154_109/OBD154_111_1:2x −0.021487184 20 OBD154_113/OBD154_115_1:4x −0.089547447 21 OBD154_117/OBD154_119_1x 0.053341863 22 OBD154_121/OBD154_123_1x −0.009481999 23 OBD154_125/OBD154_127_1:2x 0.184254198 24 OBD154_133/OBD154_135_1:2x 0.013549498 25 OBD154_137/OBD154_139_1x −0.029260042 26 OBD154_141/OBD154_143_1x 0.040466078 27 OBD154_149/OBD154_151_1:2x −0.026044566 28 OBD154_153/OBD154_155_1:8x 0.05560739 29 OBD154_157/OBD154_159_1:2x −0.111847127 30 OBD154_161/OBD154_163_1:2x −0.011075719 31 OBD154_165/OBD154_167_1x 0.052703232 32 OBD154_169/OBD154_171_1:4x 0.072817076 33 OBD154_177/OBD154_179_1x 0.023527 34 OBD154_185/OBD154_187_1x −0.028512982 35 OBD154_201/OBD154_203_1x −0.076839662 36 OBD154_205/OBD154_207_1:2x 0.101263033 37 OBD154_209/OBD154_211_1:2x 0.048686754 38 OBD154_213/OBD154_215_1:2x −0.060839024 39 OBD154_217/OBD154_219_1x 0.01900231 40 OBD154_229/OBD154_231_1x 0.10786072 41 OBD154_237/OBD154_239_1x −0.04345676 42 OBD154_245/OBD154_247_1x 0.059641358

TABLE 25.a No. Probe Loci Probe_Count_Total Probe_Count_Sig 1 CBL_11_119249760_119252653_119294588_119299643_RF CBL 24 19 2 DKK3_11_11956071_11968035_11984245_11993733_FR DKK3 54 36 3 DKK3_11_11956071_11968035_12048403_12051930_FR DKK3 54 36 4 FBXO32_8_123526212_123527874_123555254_123559065_FR FBXO32 41 26 5 KDM1A_1_23064655_23070269_23096951_23098159_FR KDM1A 25 18 6 EYA1_8_71216399_71218728_71261816_71267769_RR EYA1 139 80 7 PCK1_20_57527297_57530814_57579772_57583521_RR PCK1 36 26 8 PIK3C3_18_42070009_42072187_42088671_42094691_FF PIK3C3 141 89 9 ALDH1A2_15_58053198_58062371_58157807_58162832_RR ALDH1A2 185 100 10 CD36_7_80539507_80544315_80679651_80687690_FR CD36 169 96 11 DKK3_11_11956071_11968035_12010923_12019458_FF DKK3 54 36 12 IL1RAP_3_190489665_190498302_190560851_190563356_FR IL1RAP 160 82 13 RUNX3_1_24920810_24923822_24973522_24976037_RF RUNX3 51 24 14 PPARA_22_46101029_46102611_46241078_46244347_FR PPARA 44 26 15 SLC25A13_7_96209525_96214524_96295606_96302029_FF SLC25A13 143 99 16 PCK1_20_57527297_57530814_57551578_57557205_RR PCK1 36 26 17 MYL1_2_210288997_210291732_210359762_210362293_FF MYL1 9 5 18 C1GALT1_7_7113076_7114831_7258228_7260668_FF C1GALT1 89 4 19 COL25A1_4_109024771_109031337_109090838_109104305_RR COL25A1 134 3 20 COL5A1_9_134738485_134741113_134811418_134816113_RR COL5A1 180 0 21 DIAPH3_13_59818047_59823591_59854837_59860534_RR DIAPH3 167 1 22 FBLN2_3_13512352_13515076_13582406_13590343_RF FBLN2 93 1 23 GPC6_13_94121445_94133208_94296633_94304225_FF GPC6 166 7 24 GSN_9_121177548_121180410_121268506_121274144_FR GSN 156 6 25 GSN_9_121227501_121232628_121268506_121274144_FR GSN 156 6 26 GSN_9_121239116_121243347_121268506_121274144_FR GSN 156 6 27 LCK_1_32214585_32217213_32237144_32241139_RF LCK 24 1 28 LMO4_1_87315524_87318670_87343110_87349940_FF LMO4 105 0 29 MAPK10_4_86572598_86581486_86617317_86621940_FF MAPK10 172 2 30 MBNL1_3_152229500_152234786_152281057_152285843_FR MBNL1 144 2 31 NCAM1_11_113019160_113028536_113163748_113168132_FR NCAM1 198 3 32 PCK1_20_57527297_57530814_57570220_57572870_RR PCK1 36 0 33 PDK3_X_24441637_24447950_24480152_24481252_FR PDK3 22 0 34 PDK3_X_24441637_24447950_24490440_24491541_FR PDK3 22 0 35 PTPRC_1_198595771_198598296_198659753_198666156_RF PTPRC 184 14 36 PTPRC_1_198659753_198666156_198721093_198724578_FF PTPRC 184 14 37 RYR1_19_38410632_38413089_38495982_38499305_RR RYR1 41 6 38 THNSL2_2_88139809_88146295_88161717_88164554_FR THNSL2 29 2 39 UACA_15_70715123_70719636_70780754_70784668_RF UACA 132 1 40 ZEB1_10_31273317_31275631_31507470_31524442_FF ZEB1 163 11 41 ZFHX3_16_73147488_73153243_73182254_73184585_FF ZFHX3 170 1 42 ADRB3_8_37962724_37965269_37987735_37989039_FR ADRB3 18 0 43 AGT_1_230724515_230729957_230752057_230757333_RF AGT 45 3 44 HTR2A_13_46860092_46866824_46904346_46907815_RF HTR2A 60 5 45 SOS1_2_38982199_38993639_39061418_39066028_FF SOS1 126 0 46 ACBD6_1_180431719_180434683_180541491_180549122_RR ACBD6 173 4 47 MYH1_17_10502067_10505465_10533547_10534931_RF MYH1 103 2 48 MYOD1_11_17685862_17689487_17729653_17733608_FR MYOD1 15 1 49 NECTIN3_3_111028574_111034204_111209684_111210764_FR NECTIN3 85 4 50 ACACB_12_109146008_109150083_109236052_109237242_RR ACACB 133 2 51 ACACB_12_109236052_109237242_109268078_109273323_RR ACACB 133 2 52 IGF1R_15_98652565_98657862_98731539_98737034_RF IGF1R 176 2 53 SOCS7_17_38347510_38348776_38360864_38363420_FR SOCS7 31 1 54 STXBP4_17_55035186_55042800_55117598_55123347_RR STXBP4 141 4 55 SVEP1_9_110397951_110405969_110503630_110509758_FF SVEP1 177 7 56 EMCN_4_100636305_100649860_100744427_100745788_RR EMCN 178 2 57 ACACB_12_109146008_109150083_109185066_109187324_RR ACACB 133 2 58 FOXO1_13_40524349_40526124_40688580_40690771_RR FOXO1 89 0 59 FOXO3_6_108603215_108604436_108629992_108635481_FR FOXO3 159 2 60 FTO_16_53844989_53854574_54045378_54052319_RF FTO 153 1 61 GPC6_13_94054831_94060621_94121445_94133208_RF GPC6 166 7 62 PPP3CA_4_101055418_101067369_101247819_101259416_RR PPP3CA 153 2 63 SMAD7_18_48917335_48920290_48969505_48974578_RF SMAD7 42 0 64 SYK_9_90816328_90822228_90832284_90836084_RR SYK 160 12 65 SYK_9_90816328_90822228_90872966_90875740_RR SYK 160 12 66 TGFB2_1_218317687_218325587_218386401_218389011_FR TGFB2 130 2 67 TGFBR2_3_30566144_30567439_30694718_30698514_RR TGFBR2 191 4 68 TLR2_4_153659613_153661830_153693586_153700349_RF TLR2 32 1 69 SVEP1_9_110493529_110499578_110527410_110532406_FR SVEP1 177 7 70 MTFR1_8_65658401_65661888_65780891_65782535_RF MTFR1 91 2 71 GSN_9_121182946_121189020_121323589_121328431_FF GSN 156 6 72 MUSK_9_110648469_110652659_110747866_110751903_FR MUSK 125 1 73 PPARA_22_46128634_46134707_46231440_46235124_FR PPARA 44 0 74 PPP1R9A_7_94903925_94908776_94951930_94967018_RF PPP1R9A 166 1 75 PLCXD2_3_111633890_111638317_111672672_111677327_FR PLCXD2 144 2 76 SGCZ_8_14631157_14642508_14778176_14785491_FF SGCZ 191 11 77 SRI_7_88199682_88203042_88229166_88237101_RF SRI 57 2

TABLE 25.b No. HyperG_Stats FDR_HyperG Percent_Sig logFC AveExpr t 1 0.023815147 0.261918121 79.17 −0.426375519 −0.426375519 −4.618561579 2 0.113222201 0.567553327 66.67 −0.452190179 −0.452190179 −4.498338722 3 0.113222201 0.567553327 66.67 −0.473931719 −0.473931719 −4.801248921 4 0.279504208 0.898561555 63.41 −0.428908404 −0.428908404 −11.06651685 5 0.103914483 0.548863748 72 0.450982494 0.450982494 11.74211542 6 0.544172978 1 57.55 −0.420279402 −0.420279402 −6.888734462 7 0.052274012 0.438252195 72.22 −0.454377101 −0.454377101 −3.146677782 8 0.108139211 0.559937306 63.12 0.349058418 0.349058418 10.19574365 9 0.85625995 1 54.05 −0.42054833 −0.42054833 −8.812988665 10 0.618616868 1 56.8 0.355814357 0.355814357 4.033543511 11 0.113222201 0.567553327 66.67 −0.474435884 −0.474435884 −4.565896539 12 0.956664907 1 51.25 0.348466077 0.348466077 11.56470451 13 0.95196413 1 47.06 0.364233402 0.364233402 10.30993314 14 0.486340587 1 59.09 −0.447624697 −0.447624697 −6.45833793 15 0.00284877 0.08241485 69.23 0.351229127 0.351229127 5.941886473 16 0.052274012 0.438252195 72.22 −0.427795857 −0.427795857 −2.904768228 17 0.682316487 1 55.56 −0.389190141 −0.389190141 −13.74123239 18 0.024327419 0.687064234 4.49 −0.555546218 −0.555546218 −11.0417245 19 0.228355538 1 2.24 0.335547043 0.335547043 5.207330156 20 1 1 0 −0.481446393 −0.481446393 −3.82029126 21 0.873903179 1 0.6 0.405185839 0.405185839 2.998972245 22 0.684023987 1 1.08 −0.422325738 −0.422325738 −8.04265312 23 0.004639027 0.223094969 4.22 0.395980197 0.395980197 1.793119535 24 0.013014007 0.465546506 3.85 −0.435924362 −0.435924362 −4.024149814 25 0.013014007 0.465546506 3.85 −0.489846734 −0.489846734 −3.901621745 26 0.013014007 0.465546506 3.85 −0.490566516 −0.490566516 −4.064123806 27 0.257000004 1 4.17 0.404856809 0.404856809 4.029112137 28 1 1 0 −0.425303631 −0.425303631 −4.334227249 29 0.626639375 1 1.16 0.369477889 0.369477889 10.62330419 30 0.530285478 1 1.39 −0.423225201 −0.423225201 −5.762419013 31 0.440361719 1 1.52 −0.473418522 −0.473418522 −5.252061333 32 1 1 0 −0.443750376 −0.443750376 −3.069308332 33 1 1 0 −0.516209141 −0.516209141 −2.912953295 34 1 1 0 −0.482956676 −0.482956676 −2.845644248 35 7.93E−08 3.12E−05 7.61 0.342871898 0.342871898 12.24688433 36 7.93E−08 3.12E−05 7.61 0.353200746 0.353200746 12.71706109 37 1.05E−05 0.00164927 14.63 0.379845454 0.379845454 3.091066536 38 0.049255392 1 6.9 0.348303621 0.348303621 5.482854907 39 0.805245253 1 0.76 −0.452444827 −0.452444827 −6.645114759 40 6.24E−06 0.00122739 6.75 0.341402554 0.341402554 8.358154799 41 0.878517137 1 0.59 −0.437339546 −0.437339546 −7.571199723 42 1 1 0 −0.431801011 −0.431801011 −3.395119054 43 0.017905795 0.612689599 6.67 −0.462997504 −0.462997504 −4.192393926 44 0.000863162 0.056609039 8.33 −0.450665703 −0.450665703 −8.327533972 45 1 1 0 −0.483305844 −0.483305844 −11.1896848 46 0.165185813 1 2.31 −0.438627353 −0.438627353 −7.215605041 47 0.362024499 1 1.94 −0.433949544 −0.433949544 −7.773631426 48 0.169428566 1 6.67 −0.44490366 −0.44490366 −11.70445784 49 0.020952195 0.683779761 4.71 −0.367763769 −0.367763769 −7.284235112 50 0.488070766 1 1.5 0.37639594 0.37639594 5.784183467 51 0.488070766 1 1.5 0.361980641 0.361980641 6.812052569 52 0.63908073 1 1.14 0.376793177 0.376793177 3.580450098 53 0.318687894 1 3.23 0.325631694 0.325631694 8.979749407 54 0.096791402 1 2.84 0.347975579 0.347975579 7.974747337 55 0.006539151 0.270858531 3.95 0.328480984 0.328480984 4.835157675 56 0.645178258 1 1.12 0.319852241 0.319852241 5.68627836 57 0.488070766 1 1.5 −0.639467523 −0.639467523 −7.69815267 58 1 1 0 0.393248671 0.393248671 6.480891366 59 0.583919721 1 1.26 0.365259231 0.365259231 6.804140703 60 0.849949517 1 0.65 −0.434234901 −0.434234901 −9.879188206 61 0.004639027 0.223094969 4.22 0.528815395 0.528815395 2.192030297 62 0.563021006 1 1.31 −0.462324823 −0.462324823 −10.32420109 63 1 1 0 0.40277223 0.40277223 2.549597378 64 7.81E−07 0.000204861 7.5 0.454881152 0.454881152 6.892290381 65 7.81E−07 0.000204861 7.5 0.491854549 0.491854549 7.332798069 66 0.476152064 1 1.54 −0.427835042 −0.427835042 −9.631799551 67 0.209498358 1 2.09 0.713766505 0.713766505 5.020955434 68 0.327072861 1 3.12 0.370613279 0.370613279 12.69019114 69 0.006539151 0.270858531 3.95 −0.425150058 −0.425150058 −9.267584464 70 0.308264448 1 2.2 −0.373414166 −0.373414166 −11.79966649 71 0.013014007 0.465546506 3.85 0.360333931 0.360333931 7.597970849 72 0.787565452 1 0.8 0.386657089 0.386657089 7.586923373 73 1 1 0 0.362541486 0.362541486 2.971365926 74 0.872326654 1 0.6 0.363099567 0.363099567 3.977705912 75 0.530285478 1 1.39 0.371871445 0.371871445 9.143459938 76 2.76E−05 0.00285196 5.76 0.351857885 0.351857885 12.4599802 77 0.155413907 1 3.51 0.345097648 0.345097648 6.863477929

TABLE 25.c No. P.Value adj.P.Val B FC 1 0.000204351 0.001696324 0.420007759 0.744128913 2 0.000266954 0.002046882 0.154483715 0.730932365 3 0.000136422 0.001270248 0.822155807 0.719999735 4 0.00000000106 0.000000159 12.50758304 0.742823621 5 0.00000000057763115753262 0.000000240382974465845 13.11880883 1.366970864 6 0.00000174500366992146 0.0000602085318700566 5.184417423 0.747279887 7 0.005488024 0.018949968 −2.809655881 0.729825214 8 0.00000000406 0.000000379 11.17917387 1.27372905 9 0.0000000519795383109141 0.00000495299418442526 8.693472403 0.747140602 10 0.000716034 0.003059888 −0.936521584 1.279707733 11 0.000229703 0.001841162 0.303764249 0.719748167 12 0.000000000513 0.0000000948 13.22969486 1.273206191 13 0.00000000464664280056321 0.000000961862645683259 11.08156058 1.287197476 14 0.00000409787235536200 0.000109374 4.328897959 0.733249101 15 0.0000118 0.000224511 3.269636273 1.275646972 16 0.00932387 0.028011446 −3.317120561 0.743396676 17 0.0000000000274 0.0000000141 16.09554078 0.763558109 18 0.00000000111 0.000000163 12.47094565 0.680399404 19 0.0000510 0.000371158 1.696824449 1.26185579 20 0.001219666 0.006253664 −1.346303854 0.716259169 21 0.007408583 0.020028642 −3.214800278 1.324259482 22 0.000000161 0.00000491 7.493520599 0.746220688 23 0.089475491 0.154086604 −5.389247882 1.315836464 24 0.000771506 0.004457333 −0.895719572 0.739219971 25 0.001015971 0.005458351 −1.166748282 0.712100745 26 0.000705273 0.004168565 −0.807203494 0.711745556 27 0.0007233 0.003084781 −0.946498319 1.323957498 28 0.000385015 0.002678159 −0.20873374 0.744681988 29 0.00000000289295572819759 0.000000681985048919552 11.54687815 1.291885213 30 0.0000171628795759885 0.000292745 2.893666517 0.745755594 31 0.0000462 0.000343634 1.795697 0.7202559 32 0.006507463 0.021473733 −2.97336687 0.73522087 33 0.009159444 0.027632407 −3.300175166 0.699206673 34 0.010599052 0.030783445 −3.439002954 0.715509746 35 0.000000000196 0.0000000539 14.17658691 1.26827878 36 0.000000000104 0.0000000375 14.80248355 1.277391491 37 0.006203474 0.020718718 −2.927451691 1.301202459 38 0.0000279 0.000231594 2.302943346 1.273062829 39 0.00000241 0.0000352 4.766915889 0.73080336 40 0.0000000904 0.00000323 8.071768487 1.266987731 41 0.000000474476333843650 0.0000231189585700664 6.488080595 0.738495203 42 0.003161948 0.012613791 −2.27662634 0.741335749 43 0.00052891 0.00336987 −0.523006115 0.725477359 44 0.000000120499326458705 0.00000908377824577704 7.856562067 0.731705139 45 0.00000000126038126093866 0.000000406018047073111 12.35960543 0.715336596 46 0.000000773 0.0000152 5.912515816 0.737836287 47 0.000000265 0.00000692 6.989653482 0.740232537 48 0.000000000420 0.0000000817 13.42754235 0.734633372 49 0.000000676 0.0000139 6.047319254 0.774982819 50 0.0000163956845883121 0.000282973 2.939466958 1.298094974 51 0.00000202795176244020 0.0000670770127555545 5.033860861 1.285189092 52 0.002089314 0.00927894 −1.873258731 1.298452444 53 0.0000000302 0.00000149 9.171680821 1.253213047 54 0.000000182 0.00000536 7.367278195 1.27277339 55 0.000116599 0.000719355 0.868191804 1.25569056 56 0.0000179 0.000164182 2.745641844 1.248202703 57 0.000000306 0.00000769 6.846486395 0.641949839 58 0.00000391616567926034 0.000106263 4.374356285 1.313347482 59 0.00000205973252071508 0.0000679202407840129 5.018280323 1.288113063 60 0.00000000906782907573557 0.00000142181714589480 10.42301097 0.740086138 61 0.041519144 0.085450094 −4.70897528 1.442744064 62 0.00000000454643610867096 0.000000946006652142489 11.10299558 0.725815704 63 0.019933628 0.04923408 −4.033722222 1.322045866 64 0.00000146 0.0000245 5.268722172 1.370669886 65 0.000000615 0.0000130 6.142312649 1.406251416 66 0.0000000101 0.000000678 10.2711503 0.743376485 67 0.0000842245621504624 0.000906383 1.302982598 1.640080359 68 0.000000000161476307566624 0.0000000940784035927087 14.34965814 1.292902317 69 0.0000000242868020514695 0.00000282996756590024 9.44872473 0.744761263 70 0.000000000367 0.0000000760 13.56117136 0.771953491 71 0.000000451423921266660 0.0000224517338792905 6.53788422 1.283722998 72 0.000000460792529508426 0.0000227787899768996 6.517344279 1.307360568 73 0.008064742 0.025126002 −3.178757551 1.285688803 74 0.000856336 0.004819753 −0.998511342 1.286186246 75 0.0000000228 0.00000120 9.452862589 1.294030342 76 0.000000000146 0.0000000458 14.46288268 1.276203048 77 0.00000155 0.0000255 5.210654526 1.270236955

TABLE 25.d Loop Probe sequence No. FC_1 LS detected 60 mer 1 −1.343853172 −1 Str_train ACCGCCTCACCTCAGCTCTCCAGTGAGATCGATCCTCCCACCTAAGCTTCCCAAGTTGCT 2 −1.36811564 −1 Str_train GACACCTCCTCTCCCTTCCCTCCCCTTCTCGAGTTATCAAAATATTTTGAGAGACAGTAT 3 −1.3888894 −1 Str_train GACACCTCCTCTCCCTTCCCTCCCCTTCTCGATGGCCACATGTGGCCAGTGGCTCTCATG 4 −1.346214596 −1 End_train TGCAGAAAGTACTACAAAAAAAGAAGCTTCGAAAATGTTGGAGATGAGAGTTTCTTCACC 5 1.366970864 1 Str_control GGCAGGTGGATCATTTGAGGTCAAGAGCTCGACAGAGCAAGACACCATCTCCAAAAAGAA 6 −1.338186692 −1 Str_train TGTCCTTTCAAGGAAGGATTAGCATCCTTCGAAAGACCTATCAGGATTTCATTTGTAATG 7 −1.370191083 −1 Str_train CCTCGTCGTCCCCTCTCTTCCTCGTTCCTCGAACATCTCCAAGTCAGATAATCATAACAA 8 1.27372905 1 End_control ATCTATTATAATGATGCAATATTGTTAATCGATTCAAAGATCAAATTAATTATTAAAGCT 9 −1.338436162 −1 Str_train ATTTTAAATGTGGCATTTTAGGTTTATTTCGATTTTGCATAAATTGAAAAAGCTGGAGAT 10 1.279707733 1 End_control TGCTGAAAGAAAACACAATTTATTTAAGTCGAAATTTTGGAAAAGCCCTGATTTAAGTCA 11 −1.389374847 −1 Str_train GACACCTCCTCTCCCTTCCCTCCCCTTCTCGATCACTTTGCAAAGCTTTGTTGGCTAGGC 12 1.273206191 1 End_control TAAATAAAATTGTCTTTTTTTGTCTTTCTCGATTACAGAGAACTAAGTACATTTTAAATC 13 1.287197476 1 Str_control CTTAATTTTTTTTCTTTGAATGCCTCTATCGACAGTCTTCTCTCTACTTTCTACAGTGAA 14 −1.363793011 −1 Str_train ACACCTCACCCACCCAGCTGGGCTGGCCTCGATGCCATTAAATCATCCCGTGACCTTCCT 15 1.275646972 1 Str_control GGCAGGCGGATCATTTCAGGTCAGGAGTTCGACCTGAAATTTCCATACTAAATTTAAATA 16 −1.345176851 −1 Str_train CCTCGTCGTCCCCTCTCTTCCTCGTTCCTCGACAGGAAAGCATACGGAAAAAGTTAAAGA 17 −1.309658019 −1 End−Train AATTTCACATTGATACATTGATAGACATTCGAAATCATACACAGCATACTCTCAAACCAT 18 −1.469724979 −1 END_Train AAATGTATAAGAACAGAAGAGAATTATCTCGACATGTCTGAAAAGTATTATCAGCCCTCT 19 1.26185579 1 END_Control AAAACACCCTGAATTGGAAGAAAGAAACTCGAGGGATGAGTGTGTATCATCAAAGTCAAA 20 −1.396142686 −1 Str_Train CGCGGGGCCTTCTGGGCCAGGCGGGCCCTCGAAAAGCCCCACGCCCCCCCAGAGCTGCTG 21 1.324259482 1 END_Control AATACGTGGTCAATCTAAGGATTATAGTTCGAAAAGATTAATGATGTATTGATGACACTT 22 −1.340086139 −1 END_Train CTTGCCTAGTCTTTAATTTATTTATTTATCGACATTTTTTTCTTATCAACGAGACGATGT 23 1.315836464 1 Str_Control AATTAGACAACGACTATATGACTCTGTCTCGAGATTGGTCTTAACACACTATTGATTATT 24 −1.352777305 −1 Str_Train AAAAAGAGAAAAGCAGGTTAGCACATTGTCGACCCCGCCCCCGGGATGGGGGAACTGGCC 25 −1.404295681 −1 Str_Train AAATTTTCAAGTGTACGATATGGTATCATCGACCCCGCCCCCGGGATGGGGGAACTGGCC 26 −1.40499648 −1 Str_Train AAACTTACGATTACATTTAGAGATCACTTCGACCCCGCCCCCGGGATGGGGGAACTGGCC 27 1.323957498 1 END_Control AAGGGCTCGGGAGCTCCCTCGGCACACCTCGAGGAGTGCCAGGCATCTACTGCTCTGTCC 28 −1.342855092 −1 Str_Train CCCCTGGCTCACCTACACAAAATTGTGCTCGACTCTACTCTTAGCCCTGCTAAATAAGTA 29 1.291885213 1 Str_Control ATTATATTAGTGCTGTAATAAAATTAAGTCGACACATTTGATACTGCTTATTGGGTTATT 30 −1.34092189 −1 Str_Train TACCTTGAAAAGCTCTTCAGTATGATTATCGAGCTTTAGCCATTCTAGTAATTATTAAAA 31 −1.38839543 −1 END_Train ATGAATTAATGTTTCCTAGAAAGTTGTCTCGAAAGAAGAAAGTGTCAGGGTTCAACTGCC 32 −1.360135493 −1 Str_Train CCTCGTCGTCCCCTCTCTTCCTCGTTCCTCGATGCGGGACTGATTGTTACAGAACTGTTT 33 −1.4301923 −1 Str_Train GGGGATGGGGCCGAAATATGATTGCACTTCGAGTTTGTTTAGTTTTTATCTTCCCCATTT 34 −1.397605002 −1 Str_Train GGGGATGGGGCCGAAATATGATTGCACTTCGAACTTCAGCACCTGACCTTTGTCATCAAC 35 1.26827878 1 END_Control AGAGGCTGAGGTGAAAAGATTGTTTGAGTCGAAGATCATTGTCTCATTTTTTTACTTGTT 36 1.277391491 1 END_Control AGAGGCTGAGGTGAAAAGATTGTTTGAGTCGATACACTGAACAAGTGCCAGAGCAGAATA 37 1.301202459 1 Str_Control GGTGGGAGGATCACTTGAGGTCAGAAGTTCGATCTCCTGACCTCAAGTGATCCTCTAGCT 38 1.273062829 1 END_Control TATCAAGTTAAACATTCAGACGTCTAGGTCGACTTGAAGTTCACCTAAAGTTTTCCAGTC 39 −1.368357145 −1 END_Train ATAGTATAGAATGACAGCATGCTGGTTATCGACAAGAGTTCTTAAAAAGCCTAAATGTCA 40 1.266987731 1 END_Control ATTCCACAAATATTTGTGAGCACCATCTTCGAGCTCATTAGTTCAAGACCAGCCTGGGCA 41 −1.354104937 −1 Str_Train CTCTCAACTTTGGATGTAAGAATCATCTTCGAGATTTTGACTCTCCACCTGCCCCACAGG 42 −1.348916468 −1 Str_Train CGGTCCCTCTGCCCCGGTTACCTACCCGTCGACATGACACTTGGGTGGGGATACAGGGCC 43 −1.378402768 −1 Str_Train TCCCCCTCTTCCTCTGCCTCCCTTCCCCTCGAAAACTGATTAAAAAGAATATTGCTGGCT 44 −1.366670735 −1 Str_Train TCACTTTTATTTATCTTACTCACTTTTCTCGAGGAATTCTCAGAATTCTCCTCAACCCAC 45 −1.397943297 −1 Str_Train TTTCTTCCAACTGAGAGAATCTTAAAAATCGAAATTGGATAAGGAAAAAAGTGAAATGTG 46 −1.355314205 −1 END_Train TTTTAGTTTTATTTATTTAGTTATCATCTCGAAAAACAAACAACAATAACAGCAACCCTC 47 −1.350926837 −1 END_train GCAAGACTTTGTCTCAAAACAAAAGTGTTCGAAAAAGTCATCGTTTAAAAGGTAAAATGT 48 −1.361223214 −1 END_Train TCCATTAGCTCTGCTTTCAAATACTATATCGATGTAGCTTATGTAAAATAAATGTATTAA 49 −1.290351187 −1 END_Train TCAAAGTTACAGTTTATATAATTAGAAATCGATCTAACCTCAATTCCAGTCCCACAAATG 50 1.298094974 1 Str_Control TCAAGAAAAAATAATAATAATTTTTTTTTCGAACTTATGGCTCAAGCGATTCTCTTGCTT 51 1.285189092 1 Str_Control AAGCAAGAGAATCGCTTGAGCCATAAGTTCGATGCTGCTTTGGGAACTGAAGGTTTTTCT 52 1.298452444 1 Str_Control CGTAGAACTAAGATGTATTCAAAGTCAGTCGAAAAAGATTAGAAAAGTTCAACTCTAAGA 53 1.253213047 1 END_Control AGGCAGGCAGATCAATGAGGTTGGGAGATCGACAAGTTCAGTAATTCTGAGGTGAGTTTT 54 1.27277339 1 END_Control GTTGTTATAACTATATCATGAGACTAAGTCGAAAAAAAAAAACAATAATTTCAGCTGTAT 55 1.25569056 1 END_Control TATATTAGAAACATGTCTGAAAAAAGTATCGATAAATGTATACGTTGATGTACATTGATA 56 1.248202703 1 END_Ctrl GGTATTACCTTGATGGCCTTAAAGAAGATCGAGCCAGAGGGCCTCTGTTCATGTTTGGGC 57 −1.55775411 −1 END_train TCAAGAAAAAATAATAATAATTTTTTTTTCGATTCCTGCTACACATTTTGGCAGAATACT 58 1.313347482 1 STR_Ctrl CATGGTTTATAATCCTTTTTATACATTGTCGACACTGTATTTTCACAGATCACTCTGGAG 59 1.288113063 1 STR_Ctrl AGAACTTCCTGATATATTTTTTTTCTTTTCGAAGGTCTTAAAATGTTTTTAAACATGACC 60 −1.351194069 −1 STR_train GACTCTTAAAACAATAATATCAAACAACTCGACTTGTCATTTAGTTCTTTGGGAAGCAGT 61 1.442744064 1 STR_Ctrl AATTAGACAACGACTATATGACTCTGTCTCGACTTTAAAGCAAGTACTTCTTGTATGCTC 62 −1.377760215 −1 STR_train TCTTTGTTTCCTGTTTCCACTTCTTATTTCGATATTTATTGAGTGCTACTATATATATGC 63 1.322045866 1 STR_Ctrl TATGAATCCCTAAATGTCACACATCAAGTCGAATTATATAAGATACCCTGAAATTTAAGG 64 1.370669886 1 END_Ctrl ATGACTGTGGAAGGTTCTGATGTCTCTGTCGATGAAATGGAGAGAGGAGAAAGAAAAGAA 65 1.406251416 1 END_Ctrl ATGACTGTGGAAGGTTCTGATGTCTCTGTCGACATCATTTTTACAAATAAGACCAGATGT 66 −1.345213388 −1 END_train AATATTGCTACTGGAAAATCTGAATCTTTCGAAGAAAGCCCTTTGTAAGTTGTTTTCAAA 67 1.640080359 1 STR_Ctrl AACTATGTGACTTTTAGCTATACGAGTTTCGACTGGGTTCTAAATAGTTAATGTCATAGT 68 1.292902317 1 STR_Ctrl TAAAACTATTTTAAATGTTTTTAAAGTATCGATGTGTACTTTGACATCTGTGATGATGAT 69 −1.342712154 −1 STR_train TTATGGCTTAGAAGTAGAAAGTCATAAATCGATTCCTAAAAATTAATGAGGTGAATAGTA 70 −1.29541483 −1 END_train TTTCTATGAAGAATGTTCAAGATGCAATTCGAGCTACATACTATTATATATTTTCACAGT 71 1.283722998 1 STR_Ctrl CTCTATAAATTTACCAGAATATAAATTCTCGACTAAAAGTTCAGTTCTTCATTCCCACTA 72 1.307360568 1 STR_Ctrl ATCTTACAAAGAATAATTCTAAGAAAAGTCGAGCATTGGAGAAAATCTCCCTTTTCTTTT 73 1.285688803 1 STR_Ctrl TGTTTTTATTTTCATGTTTTAATTTTGTTCGAACTCTTGACCTCAGGTAAACCACCCACC 74 1.286186246 1 STR_Ctrl AGAACTGGTTATTGATCTATTCAGGGATTCGAAATAATAGATTATGAATAAATTATTCTG 75 1.294030342 1 END_Ctrl CTTTTTGAAGATTATAATCTATTAGTGATCGAGGCTTTTTTGCTTTTTTTTTTTTGAGAT 76 1.276203048 1 END_Ctrl CTATATGTAAGTTACAATATGTAAGGTATCGATAGTCACTGAGACTAATTTAATGTTATA 77 1.270236955 1 END_Ctrl TGTAGGCAGATTACCTGAAGTTAGGAGTTCGATTAGGAATAACCTATCATTAGAGTTGTT

TABLE 25.e Probe Location 4 kb Sequence Location No. Chr Start1 End1 Start2 End2 Chr Start1 End1 1 11 119249760 119249791 119299612 119299643 11 119249760 119253761 2 11 11968004 11968035 11984245 11984276 11 11964034 11968035 3 11 11968004 11968035 12048403 12048434 11 11964034 11968035 4 8 123527843 123527874 123555254 123555285 8 123523873 123527874 5 1 23070238 23070269 23096951 23096982 1 23066268 23070269 6 8 71216399 71216430 71261816 71261847 8 71216399 71220400 7 20 57527297 57527328 57579772 57579803 20 57527297 57531298 8 18 42072156 42072187 42094660 42094691 18 42068186 42072187 9 15 58053198 58053229 58157807 58157838 15 58053198 58057199 10 7 80544284 80544315 80679651 80679682 7 80540314 80544315 11 11 11968004 11968035 12019427 12019458 11 11964034 11968035 12 3 190498271 190498302 190560851 190560882 3 190494301 190498302 13 1 24920810 24920841 24976006 24976037 1 24920810 24924811 14 22 46102580 46102611 46241078 46241109 22 46098610 46102611 15 7 96214493 96214524 96301998 96302029 7 96210523 96214524 16 20 57527297 57527328 57551578 57551609 20 57527297 57531298 17 2 210291701 210291732 210362262 210362293 2 210287731 210291732 18 7 7114800 7114831 7260637 7260668 7 7110830 7114831 19 4 109024771 109024802 109090838 109090869 4 109024771 109028772 20 9 134738485 134738516 134811418 134811449 9 134738485 134742486 21 13 59818047 59818078 59854837 59854868 13 59818047 59822048 22 3 13512352 13512383 13590312 13590343 3 13512352 13516353 23 13 94133177 94133208 94304194 94304225 13 94129207 94133208 24 9 121180379 121180410 121268506 121268537 9 121176409 121180410 25 9 121232597 121232628 121268506 121268537 9 121228627 121232628 26 9 121243316 121243347 121268506 121268537 9 121239346 121243347 27 1 32214585 32214616 32241108 32241139 1 32214585 32218586 28 1 87318639 87318670 87349909 87349940 1 87314669 87318670 29 4 86581455 86581486 86621909 86621940 4 86577485 86581486 30 3 152234755 152234786 152281057 152281088 3 152230785 152234786 31 11 113028505 113028536 113163748 113163779 11 113024535 113028536 32 20 57527297 57527328 57570220 57570251 20 57527297 57531298 33 X 24447919 24447950 24480152 24480183 X 24443949 24447950 34 X 24447919 24447950 24490440 24490471 X 24443949 24447950 35 1 198595771 198595802 198666125 198666156 1 198595771 198599772 36 1 198666125 198666156 198724547 198724578 1 198662155 198666156 37 19 38410632 38410663 38495982 38496013 19 38410632 38414633 38 2 88146264 88146295 88161717 88161748 2 88142294 88146295 39 15 70715123 70715154 70784637 70784668 15 70715123 70719124 40 10 31275600 31275631 31524411 31524442 10 31271630 31275631 41 16 73153212 73153243 73184554 73184585 16 73149242 73153243 42 8 37965238 37965269 37987735 37987766 8 37961268 37965269 43 1 230724515 230724546 230757302 230757333 1 230724515 230728516 44 13 46860092 46860123 46907784 46907815 13 46860092 46864093 45 2 38993608 38993639 39065997 39066028 2 38989638 38993639 46 1 180431719 180431750 180541491 180541522 1 180431719 180435720 47 17 10502067 10502098 10534900 10534931 17 10502067 10506068 48 11 17689456 17689487 17729653 17729684 11 17685486 17689487 49 3 111034173 111034204 111209684 111209715 3 111030203 111034204 50 12 109146008 109146039 109236052 109236083 12 109146008 109150009 51 12 109236052 109236083 109268078 109268109 12 109236052 109240053 52 15 98652565 98652596 98737003 98737034 15 98652565 98656566 53 17 38348745 38348776 38360864 38360895 17 38344775 38348776 54 17 55035186 55035217 55117598 55117629 17 55035186 55039187 55 9 110405938 110405969 110509727 110509758 9 110401968 110405969 56 4 100636305 100636336 100744427 100744458 4 100636305 100640306 57 12 109146008 109146039 109185066 109185097 12 109146008 109150009 58 13 40524349 40524380 40688580 40688611 13 40524349 40528350 59 6 108604405 108604436 108629992 108630023 6 108600435 108604436 60 16 53844989 53845020 54052288 54052319 16 53844989 53848990 61 13 94054831 94054862 94133177 94133208 13 94054831 94058832 62 4 101055418 101055449 101247819 101247850 4 101055418 101059419 63 18 48917335 48917366 48974547 48974578 18 48917335 48921336 64 9 90816328 90816359 90832284 90832315 9 90816328 90820329 65 9 90816328 90816359 90872966 90872997 9 90816328 90820329 66 1 218325556 218325587 218386401 218386432 1 218321586 218325587 67 3 30566144 30566175 30694718 30694749 3 30566144 30570145 68 4 153659613 153659644 153700318 153700349 4 153659613 153663614 69 9 110499547 110499578 110527410 110527441 9 110495577 110499578 70 8 65658401 65658432 65782504 65782535 8 65658401 65662402 71 9 121188989 121189020 121328400 121328431 9 121185019 121189020 72 9 110652628 110652659 110747866 110747897 9 110648658 110652659 73 22 46134676 46134707 46231440 46231471 22 46130706 46134707 74 7 94903925 94903956 94966987 94967018 7 94903925 94907926 75 3 111638286 111638317 111672672 111672703 3 111634316 111638317 76 8 14642477 14642508 14785460 14785491 8 14638507 14642508 77 7 88199682 88199713 88237070 88237101 7 88199682 88203683

TABLE 25.f 4 kb Sequence Location No. Start2 End2 PCR-Primer1_ID PCR_Primer1 1 119295642 119299643 OBD142_029 ACTGAAGGTTCCCAAGTTCCCGAGAG 2 11984245 11988246 OBD142_061 GCTCCACATTTCCCAATCTAACCTGC 3 12048403 12052404 OBD142_069 GTCCCTCTGCCCTCTCTTATTGGC 4 123555254 123559255 OBD142_089 AATCTCTGTCCCCAACTGTATCTGGC 5 23096951 23100952 OBD142_137 CCCAGTCTCAGGCTTTGTCACTC 6 71261816 71265817 OBD142_081 GGCAAGTTTCCTGACCTCTCTGACAT 7 57579772 57583773 OBD142_189 TTCTCCCTCGGACGCTCATCCTC 8 42090690 42094691 OBD142_213 CTGGAACTTGTTTAGGCACTGAAGCA 9 58157807 58161808 OBD142_017 GCTGTCATTTTCAGTGATAGGCACAC 10 80679651 80683652 OBD142_037 GCTGGTTTCCTGAGAAGGTAACTC 11 12015457 12019458 OBD142_065 TTCTTGCCCTGTCCCTCTGCCCT 12 190560851 190564852 OBD142_133 AGATGCTGGCAGTCTCCCTCTTGAG 13 24972036 24976037 OBD142_253 CTGAAATCCCATAGTGAGATGCCTTC 14 46241078 46245079 OBD142_353 GCCCTTUCCAAAAACACCTCAC 15 96298028 96302029 OBD142_477 CAGGCGGATCATTTCAGGTC 16 57551578 57555579 OBD142_181 TCATCCTCCTCCACACCCGCCTA 17 210358292 210362293 OBD142_397 CAGGCGGATCATTTCAGGTC 18 7256667 7260668 OBD142_025 CACCTCAAAAGACAACCCCAGACCCA 19 109090838 109094839 OBD142_041 CTGCCCCTTTCTTTATTCCTACTTCC 20 134811418 134815419 OBD142_045 ACCCCACCAAGAGCACCTTCTGC 21 59854837 59858838 OBD142_057 CAGTCTCTGTGGCAACTCTCGTG 22 13586342 13590343 OBD142_085 CCCCATCGCTGCTGGAAACCATT 23 94300224 94304225 OBD142_113 GAGTATTTACGATGGTCAGGTGCTGC 24 121268506 121272507 OBD142_117 GACCTGTGGTTCTGACTGTCCAG 25 121268506 121272507 OBD142_121 GGGCTGGTTAGTCAGTTATCCCTTTT 26 121268506 121272507 OBD142_125 CCACTTCCCTGCCTTTTCTGGCT 27 32237138 32241139 OBD142_141 GCGGAGCCTCTTTGAACAGAAGC 28 87345939 87349940 OBD142_145 GCAACCTGGTCTCCTACCTGCTTCTA 29 86617939 86621940 OBD142_153 TAGCAGACAATCAGAGGGTTTTGC 30 152281057 152285058 OBD142_157 GCTGGTAGTTGGCTTTTGGGAAGAAC 31 113163748 113167749 OBD142_165 CAGGAGGTGTGGATTTGACTCATACT 32 57570220 57574221 OBD142_185 TCATCCTCCTCCACACCCGCCTA 33 24480152 24484153 OBD142_197 GGGAGTAGGGAGCAGAACCAGGA 34 24490440 24494441 OBD142_201 CAACAAGGAGGGAGTGACCACAAGAT 35 198662155 198666156 OBD142_233 GCAAAGGGCAGGTCATCATCATTCAA 36 198720577 198724578 OBD142_241 AAGACATAGGCACTTTGAGAGGC 37 38495982 38499983 OBD142_257 GGACAGATTTGGAGACCCATAGAAAG 38 88161717 88165718 OBD142_297 GTAACACAGGTAGGAAGGAGTGGAGC 39 70780667 70784668 OBD142_309 GTGAGGAAGGTGTAGAAGAACAGACT 40 31520441 31524442 OBD142_321 CTTGTCGTAGAGGATGCTCAGGC 41 73180584 73184585 OBD142_325 CCTGGATGTTCATTCCCACCTGG 42 37987735 37991736 OBD142_329 TACTCCTCGTTCCCTTTTCTCTC 43 230753332 230757333 OBD142_337 GCAGATTCCACAGGGCTTAC 44 46903814 46907815 OBD142_349 TTTGTCATGTTGTCCAGGCTG 45 39062027 39066028 OBD142_357 GCTGGTCTCAAAGTCCTGGC 46 180541491 180545492 OBD142_373 GCTGGTCTCAAACTCCTGGC 47 10530930 10534931 OBD142_393 AGTATTTGAGGCTGGGCATG 48 17729653 17733654 OBD142_401 TTCTTTGTCTCCCCTCTCTACTCCT 49 111209684 111213685 OBD142_405 ACAGGAAATCCAGTATCTTGGGGAAA 50 109236052 109240053 OBD142_413 ACGGTTAGAAGATTTGCCAGAGGAT 51 109268078 109272079 OBD142_417 GAATATCAAAGATGCCAGGGAGCTG 52 98733033 98737034 OBD142_445 GACGTTTCACCATGTTGCCC 53 38360864 38364865 OBD142_509 GAATGAAACTCTGAGGCCGG 54 55117598 55121599 OBD142_517 TGTGTTATCAGGATAAGATTCCAGGT 55 110505757 110509758 OBD142_521 AGGATCTTGCTGTTTGTTTCACG 56 100744427 100748428 OBD142_005 CCCTAAACCCAGTAATCCTGTGCTTC 57 109185066 109189067 OBD142_009 GCAGAAACAGGACCTCAAACGGTTAG 58 40688580 40692581 OBD142_093 AGTTTCTCTCTGTTCCCAGTTTGCTG 59 108629992 108633993 OBD142_097 GTTCCTTTGCCCTCTTCAGTGGC 60 54048318 54052319 OBD142_101 TAGCATCCTGCCTTGACTGAGGGTGA 61 94129207 94133208 OBD142_109 GAGTATTTACGATGGTCAGGTGCTGC 62 101247819 101251820 OBD142_225 GGCTCACACAGGCTTCTGGATAGGAA 63 48970577 48974578 OBD142_261 ATTACTCAGCCCCTCGGAGCCAT 64 90832284 90836285 OBD142_265 GACTCAGGGCTGGCAGTGAACGA 65 90872966 90876967 OBD142_273 GACTCAGGGCTGGCAGTGAACGA 66 218386401 218390402 OBD142_277 TTATGGAGAACATCCTCAGTGTCCTG 67 30694718 30698719 OBD142_285 CAAGAACTGACCCCAAGTCCCTG 68 153696348 153700349 OBD142_313 GGCAGCCACTTCATCCATCCAGAATC 69 110527410 110531411 OBD142_361 TGTGTTCCCACAAATTGGAAATGCC 70 65778534 65782535 OBD142_389 CCATGCTGGCATTCATCTATTTGGT 71 121324430 121328431 OBD142_433 TAGAAGTCACTCACTCCCATCCTCT 72 110747866 110751867 OBD142_449 ACAGTCAGTGATTGGCACAGAGTAA 73 46231440 46235441 OBD142_457 ACACTTTAGACAGAGTGACAGGGTC 74 94963017 94967018 OBD142_461 AGGAATGGTTACTGCTCCTCTTTGT 75 111672672 111676673 OBD142_497 AGTCCCCACAACTGCCAATG 76 14781490 14785491 OBD142_501 AGTCTAAGAGATGGTCACACCCATT 77 88233100 88237101 OBD142_513 GTTTGGGAGGCCAATGTAGG

PCR- No. Primer2_ID PCR_Primer2 GLMNET Marker 1 OBD142_031 TTAGTCTGTATGGTAGTGTGTGCCTG 0.027324192 OBD142_029.031_1x 2 OBD142_063 GTCAGAGTTGCCGATAGGTCTTGCTA 0.066643802 OBD142_061.063_1.8x 3 OBD142_071 GGTGGGTCTGACTGCCTTTCTCA −0.093076823 OBD142_069.071_1.2x 4 OBD142_091 ACATCTATCTTGCCCCTCACTCAGGT 0.004873633 OBD142_089.091_1x 5 OBD142_139 GCCTGAGGGAGCAAGTTCAACCC −0.019817526 OBD142_137.139_1.2x 6 OBD142_083 GAAGGAGGGAGGTAGGAGAGTCATTA 0.030332059 OBD142_081.083_1.4x 7 OBD142_191 GAGGAGGAGAAACTCAGAAGCCC 0.03066036 OBD142_189.191_1x 8 OBD142_215 GCACAAGACCTCACATTCTGATGGGC 0.006242977 OBD142_213.215_1.4x 9 OBD142_019 CAAAGAGAAAGGGCTGAGGATGAAGC 0.017005669 OBD142_017.019_1.2x 10 OBD142_039 CCCCTCATCTCAGTATGTTTATGTCC 0.014942824 OBD142_037.039_1x 11 OBD142_067 GCCTGGCAAGGAGTAAGCATTCG 0.067763605 OBD142_065.067_1x 12 OBD142_135 ATGCTCCCTCCCTTATCTTTTGGTA 0.006222197 OBD142_133.135_1x 13 OBD142_255 CCCCAAACTCCCAGACACATCAGAGA 0.066746082 OBD142_253.255_1.2x 14 OBD142_355 TGCTGTCAAAATGGTGCGAAT −0.026372512 OBD142_353.355_1x 15 OBD142_479 CTTACTGCAGCCTCACACTC 0.015126312 OBD142_477.479_1x 16 OBD142_183 GACAGTAAACACACCCACTCCCC 0.04064456 OBD142_181.183_1.4x 17 OBD142_399 CTTACTGCAGCCTCACACTC 0.006805912 OBD142_397.399_1x 18 OBD142_027 CCCTCACTTTCCTTCTACTCTTCAAG 0.000572834 OBD142_025.027_1/2X 19 OBD142_043 TGTTCCCTTTGTTCAACCCAGGCTAT 0.003754206 OBD142_041.043_1/2X 20 OBD142_047 ATGGGTGAGGATGCTGGCAATGC 0.002011981 OBD142_045.047_1/2X 21 OBD142_059 CCTGAATCTGCTGTGGCTTGGGC −0.003337259 OBD142_057.059_1/4X 22 OBD142_087 CCAGTAGGAGGGAAGACACGGTC 0.007164008 OBD142_085.087_1/4X 23 OBD142_115 GATTTAGGCACTACGGAGAAAAGGGC −0.005249258 OBD142_113.115_1/2x 24 OBD142_119 TATCGTCCAGGAGGCAAGGGTCC −0.001120031 OBD142_117.119_1/2x 25 OBD142_123 AGAGGAGAGCAGGCACAGGTATCGT 0.003244236 OBD142_121.123_1/8x 26 OBD142_127 TATCGTCCAGGAGGCAAGGGTCC −0.007783392 OBD142_125.127_1/2x 27 OBD142_143 GCCTCTTCCCACCAGCCTGACTT −0.005778408 OBD142_141.143_1/4x 28 OBD142_147 GATGAGGTAACCAAAGTTCAGGGAGA −0.005269663 OBD142_145.147_1/2X 29 OBD142_155 CTCTCTCCTCATCCTCCCTCCTAATA 0.003978216 OBD142_153.155_1/2x 30 OBD142_159 GGGAGCCAGAAAGATAGCAATGCCTA −0.003656603 OBD142_157.159_1/4x 31 OBD142_167 TCACTCCCTCTCTTCTCCCCTTCACT −0.005244916 OBD142_165.167_11 32 OBD142_187 CTCTGTGGCATCCCTAAATCCCG −0.005243145 OBD142_185.187_1/4X 33 OBD142_199 ACTCCTCAAGCCCAGACAATGGC −0.000856647 OBD142_197.199_1/4x 34 OBD142_203 GTCAGTTCAGGTCTGGTTTTGCCACA −0.005241372 OBD142_201.203_1/4x 35 OBD142_235 CTCTCCTTTATCCCCTACCCTGCTCA −0.003634106 OBD142_233.235_1/2x 36 OBD142_243 GGGACCCTTTCTTCTTGCTCTGAT −0.002467172 OBD142_241.243_11 37 OBD142_259 CATTCTTGACCCTCTCACTCTGTGCC −0.009961655 OBD142_257.259_1/2x 38 OBD142_299 CACCATAAAATAGGGCAAGGTCAGCA 0.004963311 OBD142_297.299_1/2x 39 OBD142_311 GGATAGAAGGCACAGTGACCCTCCT 0.002101178 OBD142_309.311_1/2x 40 OBD142_323 GGCACGCAATCTCAATCTCGGCTC −0.005202079 OBD142_321.323_11 41 OBD142_327 AGAGGGAAAGGCAGGTCGTGAGC −0.003264119 OBD142_325.327_1/4 42 OBD142_331 TGTGTGCTAGGCTGATATGGTTTG 0.001018411 OBD142_329.331_11 43 OBD142_339 AGTCTAAAGCCCATGTGAGCC −0.000807541 OBD142_337.339_1X 44 OBD142_351 CTCAGCACCAGAACTAGGGC −0.005203446 OBD142_349.351_1X 45 OBD142_359 GCTCTAGGTGCTGATGATTCAAC −0.003795912 OBD142_357.359_1/4X 46 OBD142_375 GGTCCCCACATTACATTTTGGC −0.006643376 OBD142_373.375_1X 47 OBD142_395 AGGGTGTTCTAAGAAGGCAGC −0.006900338 OBD142_393.395_1/2X 48 OBD142_403 TTTTTATTAACTGCACGGCACACCT −0.001296151 OBD142_401.403_1X 49 OBD142_407 ACTAAGAATGGATGGGGCCAATTAT −0.00075487 OBD142_405.407_1X 50 OBD142_415 GAATATCAAAGATGCCAGGGAGCTG −0.005201838 OBD142_413.415_1/2x 51 OBD142_419 CTGCACATTTCCTAGTAGGCTCTCT −0.000282666 OBD142_417.419_11 52 OBD142_447 GTCACTCCCCATTCCATCCG 0.001436473 OBD142_445.447_1/2X 53 OBD142_511 CCCATTCGTCTCTCTGAGCTG −0.001530558 OBD142_509.511_1/8x 54 OBD142_519 TTGGTGAAAGGAAGGGAGTAGAAGT 0.005722578 OBD142_517.519_11, 1/2x 55 OBD142_523 TGCCATCACACCCATGCATG −0.005188075 OBD142_521.523_1/4x 56 OBD142_007 ATTGCTGTGGAGGGAATGGTGTGC −0.003614434 OBD142_005.007_1X 57 OBD142_011 TTTTGTAAAGGGCACCCGAAGGG 0.00909588 OBD142_009.011_1/4x 58 OBD142_095 AGCATCACCTTCGTATCTTCCCCAAG −0.002626343 OBD142_093.095_1X 59 OBD142_099 GCCTGCTCTTCCCTGTTTCTGCC 0.003599622 OBD142_097.099_1/8X 60 OBD142_103 AAACAAAGCCTCACAAACTCCACAGC −0.005544516 OBD142_101.103_1x 61 OBD142_111 ATCCAAACACAGGACGAGAATAAAGC −0.010787892 OBD142_109.111_1/2x 62 OBD142_227 TTTTGTCCCTCTTCAGGCAGTGC −0.004657708 OBD142_225.227_1/2x 63 OBD142_263 GCAGAGGAGGTGGGACTTTCAGC −0.003808119 OBD142_261.263_1/x 64 OBD142_267 CTGCCTCACCCTGGCTTCTTTCA 0.005232196 OBD142_265.267_1/4X 65 OBD142_275 CCGCCACTCAGCCATTGTTTCCA −0.003175937 OBD142_273.275_1/4X 66 OBD142_279 GCTACACAAAGAGACTTCCAGTGATT 0.00931825 OBD142_277.279_1/2x 67 OBD142_287 GGTGGAGGCGAGGGATACTGCTA −0.004573651 OBD142_285.287_1/4x 68 OBD142_315 GCAAATGCTTAGGACCCAAACCCTTT 0.004668104 OBD142_313.315_11 69 OBD142_363 CACTTGCACCCCTAAAGCTATTGAAA −0.006335271 OBD142_361.363_1/2x 70 OBD142_391 AATTTTGGTTGGCAGCTGGTAGAAG 0.008864459 OBD142_389.391_1x 71 OBD142_435 CTTGAAATGCGACCAGTGGGAATTA −0.002735702 OBD142_433.435_1X 72 OBD142_451 AGGAAATAGCCCAAATGCAACTGAA −0.004744695 OBD142_449.451_11 73 OBD142_459 CTCAACTTCAAAATCGGTTGGGGAA −0.006822261 OBD142_457.459_1X 74 OBD142_463 TTTCTGTCTGCAAATCCTCCACCTA −0.002268338 OBD142_461.463_1/4X 75 OBD142_499 CGAGAAGGGTGGCTCATGAG −0.00572004 OBD142_497.499_1/2X 76 OBD142_503 ATGGAAACCCAAGTTTGCAAGGAA −0.004756155 OBD142_501.503_1X 77 OBD142_515 GCCACAAGAGATCTGGGAC −0.005511591 OBD142_513.515_1/2x

TABLE 25.h No. Location Training Odds Ratio Glmnet 1 CBL Any 7.2 0.027324192 2 DKK3 Any 8.2 0.066643802 3 DKK3 Any 8 −0.093076823 4 FBXO32 Any 2.9 0.004873633 5 KDM1A Any 8 −0.019817526 6 EYA1 Endurance 6 0.030332059 7 PCK1 Endurance 4.5 0.03066036 8 PIK3C3 Endurance 2.25 0.006242977 9 ALDH1A2 Strength 4 0.017005669 10 CD36 Strength 12 0.014942824 11 DKK3 Strength 5 0.067763605 12 IL1RAP Strength 4 0.006222197 13 RUNX3 Strength 12 0.066746082 14 ADRB3 Strength 9 −0.026372512 15 PLCXD2 Strength 9 0.015126312 16 PCK1 Strength 2 0.04064456 17 SLC25A13 Strength 2 0.006805912 18 C1GALT1 Any n/a 0.000572834 19 COL25A1 Any n/a 0.003754206 20 COL5A1 Any n/a 0.002011981 21 DIAPH3 Any n/a −0.003337259 22 FBLN2 Any n/a 0.007164008 23 GPC6 Any n/a −0.005249258 24 GSN Any n/a −0.001120031 25 GSN Any n/a 0.003244236 26 GSN Strength n/a −0.007783392 27 LCK Endurance n/a −0.005778408 28 LMO4 Any n/a −0.005269663 29 MAPK10 Any n/a 0.003978216 30 MBNL1 Any n/a −0.003656603 31 NCAM1 Endurance n/a −0.005244916 32 PCK1 Any n/a −0.005243145 33 PDK3 Any n/a −0.000856647 34 PDK3 Any n/a −0.005241372 35 PTPRC Any n/a −0.003634106 36 PTPRC Any n/a −0.002467172 37 RYR1 Any n/a −0.009961655 38 THNSL2 Endurance n/a 0.004963311 39 UACA Any n/a 0.002101178 40 ZEB1 Any n/a −0.005202079 41 ZFHX3 Any n/a −0.003264119 42 ADRB3 Any n/a 0.001018411 43 AGT Endurance n/a −0.000807541 44 HTR2A Any n/a −0.005203446 45 SOS1 Endurance n/a −0.003795912 46 ACBD6 Any n/a −0.006643376 47 MYH1 Any n/a −0.006900338 48 MYOD1 Endurance n/a −0.001296151 49 NECTIN3 Endurance n/a −0.00075487 50 ACACB Endurance n/a −0.005201838 51 ACACB Strength n/a −0.000282666 52 IGF1R Any n/a 0.001436473 53 SOCS7 Any n/a −0.001530558 54 STXBP4 Any n/a 0.005722578 55 SVEP1 Any n/a −0.005188075 56 EMCN Endurance n/a −0.003614434 57 ACACB Endurance n/a 0.00909588 58 FOXO1 Strength n/a −0.002626343 59 FOXO3 Endurance n/a 0.003599622 60 FTO Any n/a −0.005544516 61 GPC6 Endurance n/a −0.010787892 62 PPP3CA Any n/a −0.004657708 63 SMAD7 Any n/a −0.003808119 64 SYK Endurance n/a 0.005232196 65 SYK Any n/a −0.003175937 66 TGFB2 Endurance n/a 0.00931825 67 TGFBR2 Strength n/a −0.004573651 68 TLR2 Endurance n/a 0.004668104 69 SVEP1 Any n/a −0.006335271 70 MTFR1 Any n/a 0.008864459 71 GSN Any n/a −0.002735702 72 MUSK Strength n/a −0.004744695 73 PPARA Endurance n/a −0.006822261 74 PPP1R9A Any n/a −0.002268338 75 PLCXD2 Any n/a −0.00572004 76 SGC2 Endurance n/a −0.004756155 77 SRI Strength n/a −0.005511591

TABLE 26 Gene Gene name Function CBL Cbl Proto-Oncogene Pretein coding, associated with noonan syndrome-like disorder with or without juvenile myelomonocytic leukemia and juvenile myelomonocytic leukemia, related to immune response Fc epsilon Rl pathway and EGF/EGFR signaling pathway DKK3 Dickkopf WNT Signaling Pretein coding, associated with oral submucous fibrosis disease, Pathway Inhibitor 3 related to regulation of Wnt/B-catenin signaling pathways FBXO32 F-Box Protein 32 Protein coding, accociated with muscle hypertrophy and muscle tissue disease, related to class I MHC mediated antigen processing and presentation and FoxO signaling pathway KDM1A Lysine Demethylase 1A Proteing coding; Associated with cleft palate, psychomotor retardation, and distinctive facial features and Kbg syndrome; Related to signaling by Rho GTPases and coregulation of androgen receptor activity EYA1 EYA Transcriptional Protein coding, associated with otofaciocervical syndrome 1 and Coactivator And Phosphatase branchiootorenal syndrome 1, related to transcriptional 1 misregulation in cancer and DNA double-strand break repair PCK1 Phosphoenolpyruvate Protein coding; Associated with phosphoenolpyruvate Carboxykinase 1 carboxykinase deficiency, cytosolic and pepck 1 deficiency; Related to adipogenesis and AMP-activated protein kinase (AMPK) signaling PIK3C3 Phosphatidylinositol 3-Kinase Protein coding, associated with amyotrophic lateral sclerosis 1 Catalytic Subunit Type 3 disease, related to mTOR and MAPK Pathway, involved in regulation of degradative endocytic trafficking and required for the abcission step in cytokinesis, involved in trasport from early to late endosomes ALDH1A2 Aldehyde Dehydrogenase 1 Protein coding, associated with diaphragm disease and neural tube Family Member A2 defects, related to drug metabolism cytochrome P450 and vitamin A and carotenoid metabolism CD36 CD36 Molecule Protein coding, associated with platelet glycoprotein Iv deficiency and coronary heart disease 7, related to activated TLR4 signaling and hematopoietic stem cell differentiation pathways and lineage- specific markers IL1RAP Interleukin 1 Receptor Protein coding, associated with chromosome Xp21 deletion Accessory Protein syndrome and stromal keratitis, relared to bacterial infections in CF airways and IL-1 family signaling pathways RUNX3 Runt Related Transcription Protein coding, associated with testicular yolk sac tumor and Factor 3 cleidocranial dysplasia, related to sudden infant death syndrome (SIDS) susceptibility pathways and Wnt/Hedgehog/Notch PPARA Peroxisome Proliferator Protein coding, associated with fatty liver disease and alcoholic Activated Receptor Alpha cardiomyopathy, related to gene expression and regulation of cholesterol biosynthesis by SREBP SLC25A13 Solute Carrier Family 25 Protein coding, related to metabolism and protein metabolism Member 13 pathways, associated with Citrullinemia, Type Ii, Neonatal-Onset and Citrullinemia, Type Ii, Adult-Onset MYL1 Myosin Light Chain 1 Protein coding, related to ERK signaling and cytoskeleton remodeling regulation of actin cytoskeleton by Rho GTPases

TABLE 27 Number Of Protein In Protein From GeneSet Gene Set Network FDR Nodes Th17 cell 107 14 1.52E−10 RORA, FOXP3, GATA3, SMAD3, differentiation(K) NFATC3, NFATC2, NFKB1, NFKBIE, LAT, IKBKB, PPP3CA, TGFBR2,CD247, IL17A T cell receptor 105 12 1.99E−08 GRAP2, PIK3R1, NFATC3, NFATC2, signaling pathway(K) NFKB1, NFKBIE, LAT, IKBKB, PPP3CA, LCP2, CBL, CD247 Pathways in cancer(K) 397 19 7.44E−08 RB1, ETS1, IGF1R, RASSF1, CDH1, COL4A1, PIK3R1, TGFB2, SMAD3, NFKB1, BCL2, ITGB1, IKBKB, TGFBR2, LAMA2, LAMA4, CBL, TCF7L2, APC T cell activation(P) 81 10 2.03E−07 GRAP2, PIK3R1, NFATC3, NFATC2, NFKB1, LAT, IKBKB, PPP3CA, LCP2, CD247 Th1 and Th2 cell 92 10 4.55E−07 GATA3, NFATC3, NFATC2, NFKB1, differentiation(K) NFKBIE, LAT, IKBKB, PPP3CA, DLL1, CD247 TCR signaling in naïve 67 9 4.55E−07 GRAP2, PRKCE, STIM1, LAT, CD4+ T cells(N) IKBKB, LCP2, CBL, PTPN11, CD247 Chronic myeloid 73 9 8.09E−07 RB1, PIK3R1, TGFB2, SMAD3, leukemia(K) NFKB1, IKBKB, TGFBR2, CBL, PTPN11 TCR signaling in naïve 54 8 1.21E−06 GRAP2, PRKCE, STIM1, LAT, CD8+ T cells(N) IKBKB, LCP2, CBL, CD247 Small cell lung 86 9 2.54E−06 RB1, COL4A1, PIK3R1, NFKB1, cancer(K) BCL2, ITGB1, IKBKB, LAMA2, LAMA4 Fc-epsilon receptor I 62 8 2.74E−06 PIK3R1, NFATC2, NFKB1, LAT, signaling in mast IKBKB, LCP2, CBL, PTPN11 cells(N) Inflammatory bowel 65 8 3.58E−06 RORA, IL18RAP, FOXP3, GATA3, disease (IBD)(K) TGFB2, SMAD3, NFKB1, IL17A Adherens junction(K) 72 8 7.15E−06 IGF1R, CDH1, LMO7, SMAD3, WASL, TGFBR2, TCF7L2, NECTIN3 Hepatitis B(K) 146 10 1.47E−05 RB1, PIK3R1, TGFB2, SMAD3, EGR3, NFATC3, NFATC2, NFKB1, BCL2, IKBKB TGF-beta signaling 84 8 1.94E−05 ACVR1, TGFB2, SMAD3, SMAD9, pathway(K) BMPR1B, BMPR1A, DCN, TGFBR2 Neurotrophin 121 9 2.59E−05 PIK3R1, FOXO3, NFKB1, BCL2, signaling pathway(K) NFKBIE, IKBKB, IRAK3, NTRK2, PTPN11 Colorectal cancer(K) 62 7 2.85E−05 PIK3R1, TGFB2, SMAD3, BCL2, TGFBR2, TCF7L2, APC Signaling by 460 16 2.85E−05 RORA, IL18RAP, PIK3R1, GATA3, Interleukins(R) FOXO3, NFKB1, BCL2, LAT, ITGB1, IKBKB, IRAK3, ZEB1, CBL, NCAM1, PTPN11, IL17A HTLV-I infection(K) 258 12 3.78E−05 RB1, ETS1, PIK3R1, TGFB2, SMAD3, NFATC3, NFATC2, NFKB1, IKBKB, PPP3CA, TGFBR2, APC Pancreatic cancer(K) 66 7 3.78E−05 RB1, PIK3R1, TGFB2, SMAD3, NFKB1, IKBKB, TGFBR2 Osteoclast 132 9 3.88E−05 PIK3R1, TGFB2, NFATC2, differentiation(K) NFKB1, IKBKB, PPP3CA, FCGR3A,TGFBR2, LCP2 Natural killer cell 135 9 4.44E−05 PIK3R1, NFATC2, KLRD1, LAT, mediated PPP3CA, FCGR3A, LCP2, PTPN11, cytotoxicity(K) CD247 AGE-RAGE signaling 101 8 4.44E−05 PRKCE, COL4A1, PIK3R1, TGFB2, pathway in diabetic SMAD3, NFKB1, BCL2, TGFBR2 complications(K) AP-1 transcription 70 7 4.44E−05 ETS1, BCL2L11, NFATC3, NFATC2, factor network(N) ELF1, TCF7L2, AGT CDC42 signaling 70 7 4.44E−05 CDH1, PRKCE, PIK3R1, WASL, events(N) PAX6, CBL, APC ras-independent 25 5 4.95E−05 PIK3R1, KLRD1, LAT, FCGR3A, pathway in nk cell- PTPN11 mediated cytotoxicity(B) B cell receptor 73 7 5.26E−05 PIK3R1, NFATC3, NFATC2, signaling pathway(K) NFKB1, NFKBIE, IKBKB, PPP3CA Signaling pathways 142 9 5.26E−05 IGF1R, ACVR1, PIK3R1, SMAD3, regulating SMAD9, BMPR1B, BMPR1A, pluripotency of stem PAX6, APC cells(K) Angiopoietin receptor 50 6 7.08E−05 ETS1, PIK3R1, NFKB1, ITGB1, Tie2-mediated ELF1, PTPN11 signaling(N) IL2 signaling events 28 5 7.08E−05 FOXP3, PIK3R1, BCL2, ELF1, mediated by STAT5(N) PTPN11 TGF-beta signaling 80 7 7.95E−05 ACVR1, TGFB2, SMAD3, SMAD9, pathway(P) BMPR1B, BMPR1A, TGFBR2 Signaling events 80 7 7.95E−05 ETS1, CDH1, PIK3R1, WASL, mediated by CBL, PTPN11, APC Hepatocyte Growth Factor Receptor (c- Met)(N) Signaling events 52 6 8.17E−05 GRAP2, PIK3R1, FOXO3, BCL2, mediated by Stem cell CBL, PTPN11 factor receptor (c- Kit)(N) Hippo signaling 154 9 8.17E−05 RASSF1, CDH1, TGFB2, SMAD3, pathway(K) BMPR1B, BMPR1A, TGFBR2, TCF7L2, APC Toxoplasmosis(K) 118 8 9.76E−05 PIK3R1, TGFB2, NFKB1, BCL2, ITGB1, IKBKB, LAMA2, LAMA4 EPO signaling 33 5 1.31E−04 PIK3R1, NFKB1, BCL2, CBL, PTPN11 pathway(N) Prostate cancer(K) 89 7 1.41E−04 RB1, IGF1R, PIK3R1, NFKB1, BCL2, IKBKB, TCF7L2 IL2 signaling events 35 5 1.63E−04 PIK3R1, FOXO3, NFKB1, BCL2, mediated by PI3K(N) PTPN11 FoxO signaling 134 8 2.14E−04 IGF1R, PIK3R1, FOXO3, BCL2L11, pathway(K) TGFB2, SMAD3, IKBKB, TGFBR2 Chagas disease 104 7 3.32E−04 PIK3R1, TGFB2, SMAD3, NFKB1, (American IKBKB, TGFBR2, CD247 trypanosomiasis)(K) Adipocytokine 70 6 3.45E−04 ACACB, PPARGC1A, NFKB1, signaling pathway(K) NFKBIE, IKBKB, PTPN11 sumoylation as a 7 3 3.94E−04 UBE3A, CDH1, ZEB1 mechanism to modulate ctbp- dependent gene responses(B) Insulin resistance(K) 109 7 4.15E−04 PRKCE, PIK3R1, ACACB, PPARGC1A, NFKB1, IKBKB, PTPN11 Calcineurin-regulated 46 5 5.17E−04 FOXP3, GATA3, EGR3, NFATC3, NFAT-dependent NFATC2 transcription in lymphocytes(N) MAPK signaling 255 10 5.28E−04 CACNB1, DDIT3, CACNA1E, pathway(K) TGFB2, NFATC3, NFKB1, IKBKB, PPP3CA, TGFBR2, NTRK2 FGF signaling 47 5 5.28E−04 CDH1, PIK3R1, CBL, NCAM1, pathway(N) PTPN11 Integrins in 47 5 5.28E−04 IGF1R, PIK3R1, TGFBR2, CBL, angiogenesis(N) PTPN11 TCR signaling(R) 123 7 8.14E−04 GRAP2, PIK3R1, NFKB1, LAT, IKBKB, LCP2, CD247 Endometrial cancer(K) 52 5 8.48E−04 CDH1, PIK3R1, FOXO3, TCF7L2, APC PI3K-Akt signaling 341 11 1.10E−03 IGF1R, COL4A1, PIK3R1, FOXO3, pathway(K) BCL2L11, NFKB1, BCL2, ITGB1, IKBKB, LAMA2, LAMA4 Fc epsilon receptor 405 12 1.16E−03 GRAP2, PIK3R1, FOXO3, NFATC3, (FCERI) signaling(R) NFATC2, NFKB1, LAT, IKBKB, PPP3CA, LCP2, NCAM1, PTPN11 Transcriptional 180 8 1.17E−03 IGF1R, DDIT3, NFKB1, NR4A3, misregulation in TGFBR2, ZEB1, PAX7, EYA1 cancer(K) Fc gamma R-mediated 93 6 1.17E−03 PRKCE, PIK3R1, LAT, WASL, phagocytosis(K) FCGR3A, GSN ATF-2 transcription 58 5 1.17E−03 RB1, DDIT3, PPARGC1A, TGFB2, factor network(N) BCL2 Validated targets of C- 60 5 1.37E−03 DDIT3, FOXO3, SMAD3, BCL2, MYC transcriptional ITGB1 repression(N) Amoebiasis(K) 98 6 1.55E−03 COL4A1, PIK3R1, TGFB2, NFKB1, LAMA2, LAMA4 IL1-mediated signaling 34 4 1.81E−03 PIK3R1, NFKB1, IKBKB, IRAK3 events(N) BCR signaling 65 5 1.95E−03 ETS1, PIK3R1, NFKB1, IKBKB, pathway(N) PPP3CA JNK signaling in the 14 3 1.95E−03 GRAP2, LAT, LCP2 CD4+ TCR pathway(N) Atypical NF-kappaB 14 3 1.95E−03 PIK3R1, NFKB1, IKBKB pathway(N) Extracellular matrix 255 9 2.09E−03 CDH1, COL4A1, TGFB2, ITGB1, organization(R) DCN, LAMA2, LAMA4, NRXN1, NCAM1 IL23-mediated 37 4 2.25E−03 IL18RAP, PIK3R1, NFKB1, IL17A signaling events(N) Proteoglycans in 205 8 2.43E−03 IGF1R, PIK3R1, TGFB2, ITGB1, cancer(K) DCN, CBL, GPC1, PTPN11 Wnt signaling 268 9 3.00E−03 CDH1, PRKCE, NFATC3, NFATC2, pathway(P) BMPR1B, BMPR1A, PPP3CA, TCF7L2, APC FOXM1 transcription 40 4 3.01E−03 RB1, NFATC3, LAMA4, CENPF factor network(N) Bacterial invasion of 78 5 3.64E−03 CDH1, PIK3R1, ITGB1, WASL, epithelial cells(K) CBL il-2 receptor beta 44 4 3.82E−03 RB1, PIK3R1, CBL, PTPN11 chain in t cell activation(B) Axon guidance 4 2 4.06E−03 NFATC3, NFATC2 mediated by netrin(P) Insulin Pathway(N) 45 4 4.16E−03 PIK3R1, FOXO3, CBL, PTPN11 AMPK signaling 124 6 4.26E−03 IGF1R, PIK3R1, FOXO3, ACACB, pathway(K) ACACA, PPARGC1A EGFR tyrosine kinase 81 5 4.26E−03 IGF1R, PIK3R1, FOXO3, BCL2L11, inhibitor resistance(K) BCL2 Ras signaling 229 8 4.26E−03 ETS1, IGF1R, RASSF1, PIK3R1, pathway(K) NFKB1, LAT, IKBKB, PTPN11 Hypertrophic 83 5 4.26E−03 CACNB1, TGFB2, ITGB1, cardiomyopathy LAMA2, TTN (HCM)(K) the co-stimulatory 20 3 4.26E−03 PIK3R1, PTPN11, CD247 signal during t-cell activation(B) Axon guidance(K) 177 7 4.27E−03 PIK3R1, NFATC3, NFATC2, BMPR1B, ITGB1, PPP3CA, PTPN11 Type II diabetes 48 4 4.62E−03 PRKCE, PIK3R1, CACNA1E, IKBKB mellitus(K) t cell receptor 48 4 4.62E−03 PIK3R1, LAT, PTPN11, CD247 signaling pathway(B) GPVI-mediated 49 4 4.99E−03 PIK3R1, LAT, LCP2, PTPN11 activation cascade(R) MicroRNAs in 299 9 5.10E−03 RASSF1, PRKCE, BCL2L11, TGFB2, cancer(K) NFKB1, BCL2, IKBKB, ZEB1, APC influence of ras and 22 3 5.46E−03 RB1, PIK3R1, IKBKB rho proteins on g1 to s transition(B) Dilated 90 5 5.46E−03 CACNB1, TGFB2, ITGB1, LAMA2, cardiomyopathy(K) TTN Role of Calcineurin- 52 4 5.46E−03 PRKCE, NFATC3, NFATC2, BCL2 dependent NFAT signaling in lymphocytes(N) Signaling by MET(R) 52 4 5.46E−03 PIK3R1, ITGB1, CBL, PTPN11 Signaling by BMP(R) 23 3 5.46E−03 SMAD9, BMPR1B, BMPR1A role of mef2d in t-cell 23 3 5.46E−03 LAT, PTPN11, CD247 apoptosis(B) Apoptosis(K) 140 6 6.04E−03 DDIT3, PIK3R1, BCL2L11, NFKB1, BCL2, IKBKB Insulin signaling 140 6 6.04E−03 PIK3R1, ACACB, ACACA, pathway(K) PPARGC1A, IKBKB, CBL IL2-mediated signaling 54 4 6.12E−03 PRKCE, PIK3R1, BCL2, PTPN11 events(N) Longevity regulating 94 5 6.28E−03 IGF1R, PIK3R1, FOXO3, pathway(K) PPARGC1A, NFKB1 Wnt signaling 143 6 6.46E−03 SMAD3, NFATC3, NFATC2, pathway(K) PPP3CA, TCF7L2, APC Non-small cell lung 56 4 6.46E−03 RB1, RASSF1, PIK3R1, FOXO3 cancer(K) Cell adhesion 145 6 6.46E−03 CDH1, CD226, ITGB1, NRXN1, molecules (CAMs)(K) NCAM1, NECTIN3 Acute myeloid 57 4 6.46E−03 PIK3R1, NFKB1, IKBKB, TCF7L2 leukemia(K) Breast cancer(K) 146 6 6.46E−03 RB1, IGF1R, PIK3R1, DLL1, TCF7L2, APC DAP12 interactions(R) 323 9 6.46E−03 GRAP2, PRKCE, PIK3R1, FOXO3, KLRD1, LAT, LCP2, NCAM1, PTPN11 Endocrine 98 5 6.46E−03 RB1, IGF1R, PIK3R1, BCL2, DLL1 resistance(K) Focal adhesion(K) 201 7 6.46E−03 IGF1R, COL4A1, PIK3R1, BCL2, ITGB1, LAMA2, LAMA4 ALK1 signaling 26 3 6.46E−03 ACVR1, SMAD9, TGFBR2 events(N) Apoptosis signaling 26 3 6.46E−03 PRKCE, BCL2L11, BCL2 pathway(P) B cell activation(P) 59 4 7.05E−03 NFATC3, NFATC2, IKBKB, PPP3CA Cytokine-cytokine 265 8 7.11E−03 IL18RAP, ACVR1, TGFB2, receptor BMPR1B, BMPR1A, TGFBR2, interaction(K) TNFRSF25, IL17A VEGFR1 specific 27 3 7.19E−03 PIK3R1, CBL, PTPN11 signals(N) Signaling events 60 4 7.49E−03 ETS1, PIK3R1, ITGB1, WASL mediated by focal adhesion kinase(N) Signaling by the B Cell 270 8 7.99E−03 STIM1, PIK3R1, FOXO3, NFKB1, Receptor (BCR)(R) NFKBIE, IKBKB, CBL, PTPN11 Rap1 signaling 212 7 8.61E−03 IGF1R, CDH1, PIK3R1, DRD2, pathway(K) LAT, ITGB1, LCP2 EGF receptor (ErbB1) 29 3 8.80E−03 WASL, GSN, PTPN11 signaling pathway(N) Osteopontin-mediated 29 3 8.80E−03 PIK3R1, NFKB1, GSN events(N) Costimulation by the 63 4 8.94E−03 GRAP2, PIK3R1, PTPN11, CD247 CD28 family(R) Downstream signaling 64 4 9.47E−03 PRKCE, NFATC3, NFATC2, CD247 in naïve CD8+ T cells(N) IGF1 pathway(N) 30 3 9.69E−03 IGF1R, PIK3R1, PTPN11 Nectin adhesion 30 3 9.69E−03 CDH1, PIK3R1, NECTIN3 pathway(N) Shigellosis(K) 65 4 0.01 NFKB1, ITGB1, WASL, IKBKB Beta1 integrin cell 66 4 0.0101 COL4A1, ITGB1, LAMA2, LAMA4 surface interactions(N) Signalling by NGF(R) 421 10 0.0101 PRKCE, PIK3R1, FOXO3, BCL2L11, NFKB1, LAT, IKBKB, NCAM1, NTRK2, PTPN11 Renal cell 67 4 0.0101 ETS1, PIK3R1, TGFB2, PTPN11 carcinoma(K) N-cadherin signaling 33 3 0.0101 PIK3R1, GSN, PTPN11 events(N) HIV-1 Nef: Negative 33 3 0.0101 NFKB1, BCL2, CD247 effector of Fas and TNF-alpha(N) Melanoma(K) 71 4 0.011 RB1, IGF1R, CDH1, PIK3R1 Arrhythmogenic right 72 4 0.0116 CACNB1, ITGB1, LAMA2, TCF7L2 ventricular cardiomyopathy (ARVC)(K) a6b1 and a6b4 35 3 0.012 CDH1, PIK3R1, ITGB1 Integrin signaling(N) Leishmaniasis(K) 73 4 0.0121 TGFB2, NFKB1, ITGB1, FCGR3A Validated 37 3 0.014 NFATC3, NFATC2, DCN transcriptional targets of AP1 family members Fra1 and Fra2(N) GMCSF-mediated 37 3 0.014 PIK3R1, IKBKB, PTPN11 signaling events(N) ALK2 signaling 11 2 0.0148 ACVR1, SMAD9 events(N) lck and fyn tyrosine 11 2 0.0148 PTPN11, CD247 kinases in initiation of tcr activation(B) Immunoregulatory 187 6 0.0169 CDH1, CD226, KLRD1, ITGB1, interactions between FCGR3A, CD247 a Lymphoid and a non- Lymphoid cell(R) IFN-gamma 40 3 0.0173 PIK3R1, CBL, PTPN11 pathway(N) Signaling by FGFR3(R) 40 3 0.0173 PIK3R1, CBL, PTPN11 insulin signaling 12 2 0.0175 PIK3R1, PTPN11 pathway(B) C-MYB transcription 82 4 0.0183 ETS1, GATA3, BCL2, PPP3CA factor network(N) ECM-receptor 82 4 0.0183 COL4A1, ITGB1, LAMA2, LAMA4 interaction(K) Bladder cancer(K) 41 3 0.0186 RB1, RASSF1, CDH1 Signaling by FGFR4(R) 41 3 0.0186 PIK3R1, CBL, PTPN11 BMP receptor 41 3 0.0186 SMAD9, BMPR1B, BMPR1A signaling(N) human 13 2 0.0205 RB1, PIK3R1 cytomegalovirus and map kinase pathways(B) Metabolism of 13 2 0.0205 ACE2, AGT Angiotensinogen to Angiotensins(R) Fatty acid 13 2 0.0205 ACACB, ACACA biosynthesis(K) b cell survival 13 2 0.0205 PIK3R1, ITGB1 pathway(B) Beta3 integrin cell 43 3 0.0212 COL4A1, TGFBR2, LAMA4 surface interactions(N) C-type lectin receptors 139 5 0.0215 NFATC3, NFATC2, NFKB1, (CLRs)(R) IKBKB, PPP3CA IL5-mediated signaling 14 2 0.0215 PIK3R1, PTPN11 events(N) Viral carcinogenesis(K) 203 6 0.0215 RB1, UBE3A, PIK3R1, EGR3, NFKB1, GSN Epstein-Barr virus 204 6 0.0215 RB1, PIK3R1, NFKB1, BCL2, infection(K) NFKBIE, IKBKB keratinocyte 47 3 0.0215 ETS1, PRKCE, IKBKB differentiation(B) Apoptotic execution 47 3 0.0215 CDH1, GSN, APC phase(R) Ceramide signaling 48 3 0.0215 RB1, NFKB1, BCL2 pathway(N) Posttranslational 48 3 0.0215 IGF1R, CDH1, NTRK2 regulation of adherens junction stability and dissassembly(N) FoxO family 48 3 0.0215 FOXO3, BCL2L11, IKBKB signaling(N) Signaling by FGFR1(R) 49 3 0.0227 PIK3R1, CBL, PTPN11 NF-kappa B signaling 95 4 0.0228 NFKB1, BCL2, LAT, IKBKB pathway(K) role of pi3k subunit 16 2 0.0229 PIK3R1, WASL p85 in regulation of actin organization and cell migration(B) Non-alcoholic fatty 151 5 0.0235 DDIT3, PIK3R1, BCL2L11, liver disease NFKB1, IKBKB (NAFLD)(K) SHP2 signaling(N) 51 3 0.0253 IGF1R, PIK3R1, PTPN11 pten dependent cell 17 2 0.0257 PIK3R1, ITGB1 cycle arrest and apoptosis(B) Signaling by SCF-KIT(R) 290 7 0.028 GRAP2, PIK3R1, FOXO3, LAT, CBL, NCAM1, PTPN11 Fcgamma receptor 159 5 0.0289 PRKCE, PIK3R1, WASL, FCGR3A, (FCGR) dependent CD247 phagocytosis(R) Oxytocin signaling 159 5 0.0289 CACNB1, PIK3R1, NFATC3, pathway(K) NFATC2, PPP3CA Glucagon signaling 103 4 0.0301 ACACB, ACACA, PPARGC1A, pathway(K) PPP3CA HIF-1 signaling 103 4 0.0301 IGF1R, PIK3R1, NFKB1, BCL2 pathway(K) Pathogenic 55 3 0.031 CDH1, ITGB1, WASL Escherichia coli infection(K) cyclins and cell cycle 19 2 0.0318 RB1, PTPN11 regulation(B) tgf beta signaling 19 2 0.0318 CDH1, TGFB2 pathway(B) Signaling by NODAL(R) 19 2 0.0318 FOXO3, SMAD3 fas signaling pathway 19 2 0.0318 RB1, PTPN11 (cd95)(B) tumor suppressor arf 19 2 0.0318 RB1, PIK3R1 inhibits ribosomal biogenesis(B) cGMP-PKG signaling 168 5 0.0346 PRKCE, PIK3R1, NFATC3, pathway(K) NFATC2, PPP3CA cell cycle: g1/s check 21 2 0.0346 RB1, PTPN11 point(B) growth hormone 21 2 0.0346 PIK3R1, PTPN11 signaling pathway(B) E-cadherin signaling in 21 2 0.0346 CDH1, PIK3R1 keratinocytes(N) igf-1 signaling 21 2 0.0346 PIK3R1, PTPN11 pathway(B) nf-kb signaling 21 2 0.0346 NFKB1, IKBKB pathway(B) Neurotrophic factor- 60 3 0.0346 PIK3R1, NTRK2, PTPN11 mediated Trk receptor signaling(N) IL12-mediated 61 3 0.0346 IL18RAP, NFKB1, CD247 signaling events(N) VEGF signaling 61 3 0.0346 PIK3R1, NFATC2, PPP3CA pathway(K) ctcf: first multivalent 22 2 0.0346 PIK3R1, TGFB2 nuclear factor(B) Nephrin 22 2 0.0346 PIK3R1, WASL interactions(R) Incretin synthesis, 22 2 0.0346 PAX6, TCF7L2 secretion, and inactivation(R) Signaling by EGFR(R) 317 7 0.0346 PRKCE, PIK3R1, FOXO3, LAT, CBL, NCAM1, PTPN11 IL4-mediated signaling 63 3 0.0346 ETS1, PIK3R1, CBL events(N) Signaling events 63 3 0.0346 PIK3R1, CBL, PTPN11 mediated by VEGFR1 and VEGFR2(N) LPA receptor 63 3 0.0346 PRKCE, PIK3R1, NFKB1 mediated events(N) Canonical NF-kappaB 23 2 0.0346 NFKB1, IKBKB pathway(N) Signaling events 23 2 0.0346 PIK3R1, TGFB2 mediated by the Hedgehog family(N) Renin-angiotensin 23 2 0.0346 ACE2, AGT system(K) Signaling events 23 2 0.0346 ITGB1, AGT mediated by PRL(N) Tuberculosis(K) 179 5 0.0346 TGFB2, NFKB1, BCL2, PPP3CA, FCGR3A Longevity regulating 64 3 0.0346 IGF1R, PIK3R1, FOXO3 pathway - multiple species(K) Regulation of 64 3 0.0346 RB1, TGFB2, ELF1 retinoblastoma protein(N) HIF-1-alpha 65 3 0.0346 RORA, ETS1, SMAD3 transcription factor network(N) nfkb activation by 24 2 0.0346 TGFB2, IKBKB nontypeable hemophilus influenzae(B) PDGFR-beta signaling 120 4 0.0346 PRKCE, WASL, CBL, PTPN11 pathway(N) Sphingolipid signaling 120 4 0.0346 PRKCE, PIK3R1, NFKB1, BCL2 pathway(K) Glioma(K) 66 3 0.0346 RB1, IGF1R, PIK3R1 Angiogenesis(P) 66 3 0.0346 ETS1, TCF7L2, APC Signaling by PDGF(R) 328 7 0.0346 PRKCE, COL4A1, PIK3R1, FOXO3, LAT, NCAM1, PTPN11 Platelet activation(K) 122 4 0.0352 STIM1, PIK3R1, ITGB1, LCP2 VEGFR3 signaling in 25 2 0.0355 PIK3R1, ITGB1 lymphatic endothelium(N) Glypican 1 network(N) 25 2 0.0355 TGFBR2, GPC1 Epithelial cell signaling 68 3 0.0362 NFKB1, IKBKB, PTPN11 in Helicobacter pylori infection(K) Regulation of 68 3 0.0362 UBE3A, SMAD3, NFKB1 Telomerase(N) Chemokine signaling 187 5 0.0365 PIK3R1, FOXO3, NFKB1, WASL, pathway(K) IKBKB p75(NTR)-mediated 69 3 0.0377 PIK3R1, BCL2L11, IKBKB signaling(N) IL3-mediated signaling 26 2 0.0382 PIK3R1, PTPN11 events(N) IL27-mediated 26 2 0.0382 GATA3, IL17A signaling events(N) Signaling events 26 2 0.0382 FOXO3, PPARGC1A mediated by HDAC Class III(N) Endocytosis(K) 260 6 0.0384 IGF1R, TGFB2, SMAD3, WASL, TGFBR2, CBL Fc epsilon Rl signaling 70 3 0.0391 PIK3R1, LAT, LCP2 pathway(K) Cell junction 70 3 0.0391 CDH1, ITGB1, NECTIN3 organization(R) Signaling by FGFR2(R) 71 3 0.0406 PIK3R1, CBL, PTPN11 Calcium signaling in 27 2 0.041 NFATC3, NFATC2 the CD4+ TCR pathway(N) Prolactin signaling 72 3 0.0421 PIK3R1, FOXO3, NFKB1 pathway(K) Signaling by TGF-beta 73 3 0.0436 SMAD3, TGFBR2, CBL Receptor Complex(R) Reelin signaling 28 2 0.0439 PIK3R1, ITGB1 pathway(N) IL8- and CXCR1- 28 2 0.0439 PRKCE, CBL mediated signaling events(N) p73 transcription 75 3 0.0467 RB1, FOXO3, BCL2L11 factor network(N) Thyroid cancer(K) 29 2 0.0468 CDH1, TCF7L2 AlphaE beta7 integrin 3 1 0.048 CDH1 cell surface interactions(N) erk and pi-3 kinase are 30 2 0.0499 PIK3R1, ITGB1 necessary for collagen binding in corneal epithelia(B) Regulation of nuclear 77 3 0.05 GATA3, FOXO3, SMAD3 SMAD2/3 signaling(N) IL12 signaling 31 2 0.053 IL18RAP, CD247 mediated by STAT4(N) Antifolate 31 2 0.053 NFKB1, IKBKB resistance(K) trefoil factors initiate 31 2 0.053 PIK3R1, IKBKB mucosal healing(B) Regulation of nuclear 80 3 0.0551 CDH1, TCF7L2, APC beta catenin signaling and target gene transcription(N) Toll-Like Receptors 141 4 0.056 NFKB1, IKBKB, IRAK3, PTPN11 Cascades(R) Netrin-mediated 32 2 0.0562 PIK3R1, WASL signaling events(N) Propanoate 32 2 0.0562 ACACB, ACACA metabolism(K) L1CAM interactions(R) 82 3 0.0587 ITGB1, CHL1, NCAM1 Apoptosis - multiple 33 2 0.0594 BCL2L11, BCL2 species(K) Regulation of actin 214 5 0.0605 PIK3R1, ITGB1, WASL, GSN, APC cytoskeleton(K) phospholipase c 4 1 0.0638 PIK3R1 signaling pathway(B) signal transduction 35 2 0.0662 TGFB2, IKBKB through il1r(B) Signaling mediated by 35 2 0.0662 DDIT3, PPARGC1A p38-alpha and p38- beta(N) Salmonella 86 3 0.0662 NFKB1, WASL, DYNC1I1 infection(K) Trk receptor signaling 36 2 0.0696 PIK3R1, FOXO3 mediated by PI3K and PLC-gamma(N) mechanism of gene 36 2 0.0696 RB1, PPARGC1A regulation by peroxisome proliferators via ppara(B) inactivation of gsk3 by 36 2 0.0696 PIK3R1, IKBKB akt causes accumulation of b- catenin in alveolar macrophages(B) E-cadherin signaling in 36 2 0.0696 CDH1, PIK3R1 the nascent adherens junction(N) Retinoid metabolism 38 2 0.0768 GPC1, GPC6 and transport(R) Nucleotide-binding 38 2 0.0768 BCL2, IKBKB domain, leucine rich repeat containing receptor (NLR) signaling pathways(R) EPHB forward 38 2 0.0768 PIK3R1, WASL signaling(N) Integration of energy 92 3 0.0783 ACACB, CACNA1E, ACACA metabolism(R) cyclin e destruction 5 1 0.0794 RB1 pathway(B) Signaling events 39 2 0.0805 PIK3R1, PTPN11 regulated by Ret tyrosine kinase(N) Pyruvate 39 2 0.0805 ACACB, ACACA metabolism(K) Oxidative stress 40 2 0.0842 DDIT3, BCL2 response(P) Class I PI3K signaling 40 2 0.0842 FOXO3, LAT events(N) Intrinsic Pathway for 41 2 0.0849 BCL2L11, BCL2 Apoptosis(R) Netrin-1 signaling(R) 42 2 0.0849 WASL, PTPN11 Stabilization and 42 2 0.0849 IGF1R, CDH1 expansion of the E- cadherin adherens junction(N) Plasma membrane 42 2 0.0849 IGF1R, PIK3R1 estrogen receptor signaling(N) Inflammatory 99 3 0.0849 PRKCE, PIK3R1, HTR2A mediator regulation of TRP channels(K) proteolysis and 6 1 0.0849 DLL1 signaling pathway of notch(B) overview of 6 1 0.0849 RB1 telomerase rna component gene hterc transcriptional regulation(B) e2f1 destruction 6 1 0.0849 RB1 pathway(B) regulation of p27 6 1 0.0849 RB1 phosphorylation during cell cycle progression(B) cell to cell adhesion 6 1 0.0849 PTPN11 signaling(B) Alternative NF-kappaB 6 1 0.0849 NFKB1 pathway(N) Presenilin action in 45 2 0.0849 DLL1, APC Notch and Wnt signaling(N) TNF receptor signaling 46 2 0.0849 NFKB1, IKBKB pathway(N) cbl mediated ligand- 7 1 0.0849 CBL induced downregulation of egf receptors pathway(B) Depolarization of the 7 1 0.0849 CACNA1E Presynaptic Terminal Triggers the Opening of Calcium Channels(R) Toll-like receptor 106 3 0.0849 PIK3R1, NFKB1, IKBKB signaling pathway(K) IL6-mediated signaling 47 2 0.0849 PIK3R1, PTPN11 events(N) TGF-beta receptor 47 2 0.0849 SMAD3, TGFBR2 signaling(N) Signaling by Type 1 255 5 0.0849 IGF1R, PIK3R1, LAT, NCAM1, Insulin-like Growth PTPN11 Factor 1 Receptor (IGF1R)(R) Cardiac conduction(R) 107 3 0.0849 CACNB1, STIM1, TRDN Heterotrimeric G- 108 3 0.0849 PRKCE, CACNA1E, DRD2 protein signaling pathway-Gq alpha and Go alpha mediated pathway(P) Cocaine addiction(K) 49 2 0.0849 DRD2, NFKB1 TNF signaling 110 3 0.0849 PIK3R1, NFKB1, IKBKB pathway(K) Calcium signaling 182 4 0.0849 STIM1, CACNA1E, HTR2A, pathway(K) PPP3CA PIP3 activates AKT 111 3 0.0849 PIK3R1, FOXO3, PTPN11 signaling(R) chaperones modulate 8 1 0.0849 RB1 interferon signaling pathway(B) a4b7 Integrin 8 1 0.0849 ITGB1 signaling(N) Amyotrophic lateral 51 2 0.0849 BCL2, PPP3CA sclerosis (ALS)(K) Signaling events 52 2 0.0849 PIK3R1, LAT mediated by PTP1B(N) Caspase cascade in 52 2 0.0849 BCL2, GSN apoptosis(N) Notch signaling 52 2 0.0849 GATA3, DLL1 pathway(N) Leukocyte 116 3 0.0849 PIK3R1, ITGB1, PTPN11 transendothelial migration(K) Regulation of 53 2 0.0849 ACACB, ACACA cholesterol biosynthesis by SREBP (SREBF)(R) btg family proteins 9 1 0.0849 RB1 and cell cycle regulation(B) proteasome 9 1 0.0849 UBE3A complex(B) Interleukin signaling 55 2 0.0849 FOXO3, IKBKB pathway(P) Basal cell 55 2 0.0849 TCF7L2, APC carcinoma(K) Fatty acid, 195 4 0.0849 RORA, ACACA, PPARGC1A, triacylglycerol, and AGT ketone body metabolism(R) GP1b-IX-V activation 10 1 0.0849 PIK3R1 signalling(R) cxcr4 signaling 10 1 0.0849 PIK3R1 pathway(B) cardiac protection 10 1 0.0849 PRKCE against ros(B) Cell cycle(K) 124 3 0.0849 RB1, TGFB2, SMAD3 Platelet 59 2 0.0849 STIM1, PTPN11 homeostasis(R) PI Metabolism(R) 59 2 0.0849 PIK3R1, MTMR7 Gastrin-CREB 376 6 0.0849 PRKCE, PIK3R1, LAT, HTR2A, signalling pathway via NCAM1, AGT PKC and MAPK(R) il-7 signal 11 1 0.0853 PIK3R1 transduction(B) Signaling by 11 1 0.0853 DLL1 NOTCH4(R) Signaling by 11 1 0.0853 DLL1 NOTCH3(R) protein kinase a at the 11 1 0.0853 PRKCE centrosome(B) rb tumor 11 1 0.0853 RB1 suppressor/checkpoint signaling in response to dna damage(B) regulation of 11 1 0.0853 RB1 transcriptional activity by pml(B) Alpha6 beta4 integrin- 11 1 0.0853 LAMA2 ligand interactions(N) how does salmonella 11 1 0.0853 WASL hijack a cell(B) Coregulation of 60 2 0.0855 UBE3A, GSN Androgen receptor activity(N) Cell surface 208 4 0.089 PIK3R1, ITGB1, GPC1, PTPN11 interactions at the vascular wall(R) Direct p53 132 3 0.0923 RB1, BCL2, APC effectors(N) epo signaling 12 1 0.0927 PTPN11 pathway(B) trka receptor signaling 12 1 0.0927 PIK3R1 pathway(B) Signal regulatory 12 1 0.0927 PTPN11 protein (SIRP) family interactions(R) p53 signaling 12 1 0.0927 RB1 pathway(B) Hepatitis C(K) 133 3 0.0939 PIK3R1, NFKB1, IKBKB Cytosolic DNA-sensing 64 2 0.0954 NFKB1, IKBKB pathway(K) mTOR signaling 64 2 0.0954 PPARGC1A, IKBKB pathway(N) Renin secretion(K) 65 2 0.0979 PPP3CA, AGT il 6 signaling 13 1 0.1 PTPN11 pathway(B) il 3 signaling 13 1 0.1 PTPN11 pathway(B) Platelet Adhesion to 13 1 0.1 ITGB1 exposed collagen(R) Signaling by Activin(R) 13 1 0.1 SMAD3 double stranded rna 13 1 0.1 IKBKB induced gene expression(B) multiple antiapoptotic 13 1 0.1 PIK3R1 pathways from igf-1r signaling lead to bad phosphorylation(B) Circadian Clock(R) 67 2 0.1029 RORA, PPARGC1A Cytosolic sensors of 67 2 0.1029 NFKB1, IKBKB pathogen-associated DNA (R) RET signaling(R) 222 4 0.1063 PIK3R1, LAT, NCAM1, PTPN11 Degradation of beta- 70 2 0.1107 TCF7L2, APC catenin by the destruction complex(R) RIG-I-like receptor 70 2 0.1107 NFKB1, IKBKB signaling pathway(K) Deubiquitination(R) 226 4 0.1116 GATA3, SMAD3, TGFBR2, APC Inflammation 71 2 0.1133 PRKCE, IKBKB mediated by chemokine and cytokine signaling pathway(P) telomeres telomerase 15 1 0.1145 RB1 cellular aging and immortality(B) Prolactin receptor 15 1 0.1145 PTPN11 signaling(R) ucalpain and friends in 15 1 0.1145 ITGB1 cell spread(B) Interferon-gamma 15 1 0.1145 PTPN11 signaling pathway(P) NCAM signaling for 231 4 0.1183 CACNB1, COL4A1, LAT, NCAM1 neurite out-growth(R) Interferon gamma 73 2 0.1185 NCAM1, PTPN11 signaling(R) Metabolism of water- 73 2 0.1185 ACACB, ACACA soluble vitamins and cofactors(R) Adrenergic signaling in 149 3 0.1207 CACNB1, PIK3R1, BCL2 cardiomyocytes(K) bone remodeling(B) 16 1 0.1216 IKBKB nerve growth factor 16 1 0.1216 PIK3R1 pathway (ngf)(B) LPA4-mediated 16 1 0.1216 PRKCE signaling events(N) RAF-independent 16 1 0.1216 PTPN11 MAPK1/3 activation(R) downregulated of 16 1 0.1216 CDH1 mta-3 in er-negative breast tumors(B) y branching of actin 16 1 0.1216 WASL filaments(B) akt signaling 16 1 0.1216 PIK3R1 pathway(B) the igf-1 receptor and 16 1 0.1216 PIK3R1 longevity(B) role of nicotinic 16 1 0.1216 PIK3R1 acetylcholine receptors in the regulation of apoptosis(B) Platinum drug 75 2 0.1239 PIK3R1, BCL2 resistance(K) Pertussis(K) 76 2 0.1266 NFKB1, ITGB1 control of skeletal 17 1 0.1287 PIK3R1 myogenesis by hdac and calcium/calmodulin- dependent kinase (camk)(B) phosphoinositides and 17 1 0.1287 PRKCE their downstream targets(B) Peroxisomal lipid 17 1 0.1287 AGPS metabolism(R) gata3 participate in 17 1 0.1287 GATA3 activating the th2 cytokine genes expression(B) RIG-I/MDA5 mediated 77 2 0.1293 NFKB1, IKBKB induction of IFN- alpha/beta pathways(R) Phagosome(K) 154 3 0.1297 ITGB1, FCGR3A, DYNC1I1 mTOR signaling 154 3 0.1297 IGF1R, PIK3R1, IKBKB pathway(K) Glucocorticoid 78 2 0.132 GATA3, NFKB1 receptor regulatory network(N) EPHA2 forward 18 1 0.1357 PIK3R1 signaling(N) Metabolism of nitric 18 1 0.1357 WASL oxide(R) Degradation of beta 18 1 0.1357 APC catenin(N) Regulation of 18 1 0.1357 SMAD3 cytoplasmic and nuclear SMAD2/3 signaling(N) mets affect on 18 1 0.1357 ETS1 macrophage differentiation(B) VEGF signaling 18 1 0.1357 ETS1 pathway(P) regulation of pgc- 18 1 0.1357 PPARGC1A 1a(B) Integrin signalling 158 3 0.137 COL4A1, PIK3R1, ITGB1 pathway(P) Jak-STAT signaling 158 3 0.137 PIK3R1, BCL2, PTPN11 pathway(K) CXCR4-mediated 80 2 0.1374 PTPN11, CD247 signaling events(N) sprouty regulation of 19 1 0.1427 CBL tyrosine kinase signals(B) EGF receptor signaling 82 2 0.143 PRKCE, CBL pathway(P) Visual 83 2 0.1457 GPC1, GPC6 phototransduction(R) Transcriptional 84 2 0.1485 PPARGC1A, NFKB1 regulation of white adipocyte differentiation(R) Canonical Wnt 20 1 0.1497 APC signaling pathway(N) tnf/stress related 20 1 0.1497 IKBKB signaling(B) regulation of bad 20 1 0.1497 PIK3R1 phosphorylation(B) egf signaling 21 1 0.1565 PIK3R1 pathway(B) erk1/erk2 mapk 21 1 0.1565 PTPN11 signaling pathway(B) segmentation clock(B) 21 1 0.1565 DLL1 PDGFR-alpha signaling 21 1 0.1565 PIK3R1 pathway(N) how progesterone 21 1 0.1565 PTPN11 initiates the oocyte maturation(B) regulation of ck1/cdk5 21 1 0.1565 DRD2 by type 1 glutamate receptors(B) NOD-like receptor 170 3 0.1597 NFKB1, BCL2, IKBKB signaling pathway(K) ErbB signaling 88 2 0.1598 PIK3R1, CBL pathway(K) Gap junction(K) 88 2 0.1598 DRD2, HTR2A stathmin and breast 22 1 0.1633 CD247 cancer resistance to antimicrotubule agents(B) ras signaling 22 1 0.1633 PIK3R1 pathway(B) inhibition of cellular 22 1 0.1633 PIK3R1 proliferation by gleevec(B) Other types of O- 22 1 0.1633 COLGALT2 glycan biosynthesis(K) TRAIL signaling 22 1 0.1633 IKBKB pathway(N) Protein digestion and 90 2 0.1655 ACE2, COL4A1 absorption(K) Rheumatoid 90 2 0.1655 TGFB2, IL17A arthritis(K) Influenza A(K) 175 3 0.1695 PIK3R1, NFKB1, IKBKB Signaling by Robo 23 1 0.1701 GPC1 receptor(R) Effects of PIP2 23 1 0.1701 PRKCE hydrolysis(R) alk in cardiac 23 1 0.1701 TGFB2 myocytes(B) regulation of eif-4e 23 1 0.1701 PIK3R1 and p70s6 kinase(B) role of erk5 in 23 1 0.1701 PIK3R1 neuronal survival pathway(B) FGF signaling 92 2 0.1712 PRKCE, PTPN11 pathway(P) corticosteroids and 24 1 0.1768 PIK3R1 cardioprotection(B) mtor signaling 24 1 0.1768 PIK3R1 pathway(B) Hypoxia response via 24 1 0.1768 PIK3R1 HIF activation(P) transcription factor 24 1 0.1768 PIK3R1 creb and its extracellular signals(B) Ephrin B reverse 24 1 0.1768 PIK3R1 signaling(N) skeletal muscle 24 1 0.1768 PIK3R1 hypertrophy is regulated via akt-mtor pathway(B) Alpha9 beta1 integrin 24 1 0.1768 ITGB1 signaling events(N) Nongenotropic 25 1 0.1835 PIK3R1 Androgen signaling(N) EndogenousTLR 25 1 0.1835 IKBKB signaling(N) fc epsilon receptor i 25 1 0.1835 PIK3R1 signaling in mast cells(B) Nephrin/Neph1 25 1 0.1835 WASL signaling in the kidney podocyte(N) tpo signaling 25 1 0.1835 PIK3R1 pathway(B) Signaling by Insulin 277 4 0.1872 PIK3R1, LAT, NCAM1, PTPN11 receptor(R) Progesterone- 98 2 0.1886 IGF1R, PIK3R1 mediated oocyte maturation(K) Herpes simplex 185 3 0.1896 NFKB1, IKBKB, PTPN11 infection(K) S1P2 pathway(N) 26 1 0.1901 PIK3R1 mcalpain and friends 26 1 0.1901 ITGB1 in cell motility(B) Maturity onset 26 1 0.1901 PAX6 diabetes of the young(K) bioactive peptide 26 1 0.1901 PIK3R1 induced signaling pathway(B) RXR and RAR 26 1 0.1901 BCL2 heterodimerization with other nuclear receptor(N) pdgf signaling 26 1 0.1901 PIK3R1 pathway(B) PI3 kinase pathway(P) 26 1 0.1901 FOXO3 Phosphatidylinositol 99 2 0.1915 PIK3R1, MTMR7 signaling system(K) DNA 27 1 0.1966 RB1 Damage/Telomere Stress Induced Senescence(R) thrombin signaling 27 1 0.1966 PIK3R1 and protease- activated receptors(B) Choline metabolism in 101 2 0.1973 PIK3R1, WASL cancer(K) Signaling by 28 1 0.2031 DLL1 NOTCH2(R) role of erbb2 in signal 28 1 0.2031 PIK3R1 transduction and oncology(B) vegf hypoxia and 28 1 0.2031 PIK3R1 angiogenesis(B) Dorso-ventral axis 28 1 0.2031 ETS1 formation(K) Hippo signaling 29 1 0.2096 RASSF1 pathway-multiple species(K) CD40/CD40L 29 1 0.2096 NFKB1 signaling(N) Response to elevated 106 2 0.2121 TGFB2, TTN platelet cytosolic Ca2+(R) ceramide signaling 30 1 0.2159 IKBKB pathway(B) Regulation of CDC42 30 1 0.2159 APC activity(N) cAMP signaling 200 3 0.2208 PIK3R1, DRD2, NFKB1 pathway(K) Circadian rhythm(K) 31 1 0.2223 RORA amb2 Integrin 31 1 0.2223 NFKB1 signaling(N) Striated Muscle 31 1 0.2223 TTN Contraction(R) Detoxification of 31 1 0.2223 PRDX6 Reactive Oxygen Species(R) phospholipids as 31 1 0.2223 PIK3R1 signalling intermediaries(B) Regulation of beta-cell 31 1 0.2223 PAX6 development(R) Mucin type O-glycan 31 1 0.2223 C1GALT1 biosynthesis(K) p38 mapk signaling 31 1 0.2223 DDIT3 pathway(B) role of egf receptor 31 1 0.2223 IKBKB transactivation by gpcrs in cardiac hypertrophy(B) EPHA forward 31 1 0.2223 CBL signaling(N) Alzheimer disease- 111 2 0.2269 CDH1, TCF7L2 presenilin pathway(P) Cholinergic synapse(K) 111 2 0.2269 PIK3R1, BCL2 Oncogene Induced 32 1 0.2286 ETS1 Senescence(R) HIF-2-alpha 32 1 0.2286 ETS1 transcription factor network(N) Syndecan-4-mediated 32 1 0.2286 ITGB1 signaling events(N) FAS (CD95) signaling 32 1 0.2286 IKBKB pathway(N) DAG and IP3 32 1 0.2286 PRKCE signaling(R) toll-like receptor 32 1 0.2286 IKBKB pathway(B) Syndecan-2-mediated 32 1 0.2286 ITGB1 signaling events(N) Noncanonical Wnt 32 1 0.2286 NFATC2 signaling pathway(N) Beta-catenin 112 2 0.2299 PPP3CA, TCF7L2 independent WNT signaling(R) Alpha4 beta1 integrin 33 1 0.2348 ITGB1 signaling events(N) integrin signaling 33 1 0.2348 ITGB1 pathway(B) FAS signaling 33 1 0.2348 GSN pathway(P) Signaling by Leptin(R) 209 3 0.24 LAT, NCAM1, PTPN11 IL8- and CXCR2- 34 1 0.241 CBL mediated signaling events(N) actions of nitric oxide 34 1 0.241 PIK3R1 in the heart(B) Arf6 trafficking 34 1 0.241 CDH1 events(N) Clathrin-mediated 117 2 0.2448 WASL, CBL endocytosis(R) Prion diseases(K) 35 1 0.2471 NCAM1 Internalization of 35 1 0.2471 CBL ErbB1(N) Class I PI3K signaling 35 1 0.2471 FOXO3 events mediated by Akt(N) African 35 1 0.2471 LAMA4 trypanosomiasis(K) Signaling events 35 1 0.2471 ITGB1 mediated by TCPTP(N)

TABLE 28 Number Of Protein In Protein From GeneSet Gene Set Network FDR Nodes BCR signaling 65 7 1.04E−05 ETS1, SYK, CARD11, PIK3R1, PAG1, pathway(N) NFKB1, PTPRC Pathways in cancer(K) 397 13 1.04E−05 GSK3B, ETS1, FGF2, IGF1R, CASP9, TGFBR2, COL4A2, COL4A1, LAMA2, CXCR4, PIK3R1, TGFB2, NFKB1 T cell receptor signaling 105 7 1.16E−04 GSK3B, PRKCQ, CARD11, PIK3R1, pathway(K) NFATC2, NFKB1, PTPRC TCR signaling in naïve 67 6 1.16E−04 STIM1, PRKCQ, CARD11, STK39, CD4+ T cells(N) PAG1, PTPRC B cell receptor signaling 73 6 1.51E−04 GSK3B, SYK, CARD11, PIK3R1, pathway(K) NFATC2, NFKB1 Extracellular matrix 255 9 2.72E−04 FGF2, DCN, COL4A2, COL4A1, organization(R) LAMA2, COL13A1, FBLN2, NCAM1, TGFB2 Small cell lung cancer(K) 86 6 2.72E−04 CASP9, COL4A2, COL4A1, LAMA2, PIK3R1, NFKB1 Angiopoietin receptor 50 5 2.72E−04 ETS1, FGF2, ELF1, PIK3R1, NFKB1 Tie2-mediated signaling(N) PI3K-Akt signaling 341 10 2.72E−04 GSK3B, FGF2, IGF1R, CASP9, SYK, CO pathway(K) L4A2, COL4A1, LAMA2, PIK3R1, NFKB1 TCR signaling in naïve 54 5 3.35E−04 STIM1, PRKCQ, CARD11, PAG1, CD8+ T cells(N) PTPRC Amoebiasis(K) 98 6 3.61E−04 COL4A2, COL4A1, LAMA2, PIK3R1, TGFB2, NFKB1 AGE-RAGE signaling 101 6 3.97E−04 TGFBR2, COL4A2, COL4A1, PIK3R1, pathway in diabetic TGFB2, NFKB1 complications(K) Colorectal cancer(K) 62 5 4.64E−04 GSK3B, CASP9, TGFBR2, PIK3R1, TGFB2 Th17 cell 107 6 4.64E−04 RORA, IL1RAP, TGFBR2, PRKCQ, differentiation(K) NFATC2, NFKB1 Insulin resistance(K) 109 6 4.84E−04 GSK3B, PYGM, PRKCQ, PIK3R1, ACACB, NFKB1 Pancreatic cancer(K) 66 5 5.40E−04 CASP9, TGFBR2, PIK3R1, TGFB2, NFKB1 Fc epsilon receptor 405 10 6.24E−04 GSK3B, FGF2, CASP9, SYK, PRKCQ, (FCERI) signaling(R) CARD11, PIK3R1, NCAM1, NFATC2, NFKB1 TCR signaling(R) 123 6 7.96E−04 PRKCQ, CARD11, PIK3R1, PAG1, NFKB1, PTPRC Osteoclast 132 6 1.03E−03 SYK, TGFBR2, PIK3R1, TGFB2, differentiation(K) NFATC2, NFKB1 Signaling by the B Cell 270 8 1.03E−03 GSK3B, FGF2, CASP9, SYK, STIM1, Receptor (BCR)(R) CARD11, PIK3R1, NFKB1 Atypical NF-kappaB 14 3 1.03E−03 SYK, PIK3R1, NFKB1 pathway(N) T cell activation(P) 81 5 1.03E−03 PRKCQ, PIK3R1, NFATC2, NFKB1, PTPRC Prostate cancer(K) 89 5 1.49E−03 GSK3B, IGF1R, CASP9, PIK3R1, NFKB1 Hepatitis B(K) 146 6 1.49E−03 CASP9, PIK3R1, TGFB2, EGR3, NFATC2, NFKB1 Integrins in 47 4 1.56E−03 FGF2, IGF1R, TGFBR2, PIK3R1 angiogenesis(N) Fc-epsilon receptor I 62 4 4.28E−03 SYK, PIK3R1, NFATC2, NFKB1 signaling in mast cells(N) HTLV-I infection(K) 258 7 4.28E−03 GSK3B, ETS1, TGFBR2, PIK3R1, TGFB2, NFATC2, NFKB1 Regulation of 64 4 4.48E−03 ELF1, MYL1, MYOD1, TGFB2 retinoblastoma protein(N) Toxoplasmosis(K) 118 5 4.49E−03 CASP9, LAMA2, PIK3R1, TGFB2, NFKB1 Osteopontin-mediated 29 3 5.96E−03 SYK, PIK3R1, NFKB1 events(N) Adherens junction(K) 72 4 5.96E−03 WASL, IGF1R, TGFBR2, NECTIN3 Focal adhesion(K) 201 6 5.96E−03 GSK3B, IGF1R, COL4A2, COL4A1, LAMA2, PIK3R1 IGF1 pathway(N) 30 3 5.96E−03 IGF1R, GRB10, PIK3R1 Chronic myeloid 73 4 5.96E−03 TGFBR2, PIK3R1, TGFB2, NFKB1 leukemia(K) FoxO signaling 134 5 6.50E−03 IGF1R, TGFBR2, PIK3R1, TGFB2, pathway(K) FBXO32 IL1-mediated signaling 34 3 7.79E−03 IL1RAP, PIK3R1, NFKB1 events(N) Signaling pathways 142 5 7.79E−03 GSK3B, FGF2, IGF1R, PIK3R1, regulating pluripotency BMPR1B of stem cells(K) EGFR tyrosine kinase 81 4 8.11E−03 GSK3B, FGF2, IGF1R, PIK3R1 inhibitor resistance(K) TGF-beta signaling 84 4 9.27E−03 DCN, TGFBR2, TGFB2, BMPR1B pathway(K) Signaling by PDGF(R) 328 7 0.0113 GSK3B, FGF2, CASP9, COL4A2, COL4A1, PIK3R1, NCAM1 Th1 and Th2 cell 92 4 0.0113 MAML2, PRKCQ, NFATC2, NFKB1 differentiation(K) Fc gamma R-mediated 93 4 0.0113 WASL, SYK, PIK3R1, PTPRC phagocytosis(K) cxcr4 signaling 10 2 0.0113 CXCR4, PIK3R1 pathway(B) NF-kappa B signaling 95 4 0.0122 SYK, PRKCQ, CARD11, NFKB1 pathway(K) Calcineurin-regulated 46 3 0.0152 PRKCQ, EGR3, NFATC2 NFAT-dependent transcription in lymphocytes(N) Endocytosis(K) 260 6 0.0155 WASL, IGF1R, TGFBR2, CXCR4, TGFB2, EHD1 Chagas disease 104 4 0.0155 TGFBR2, PIK3R1, TGFB2, NFKB1 (American trypanosomiasis)(K) Axon guidance(K) 177 5 0.0155 GSK3B, CXCR4, PIK3R1, NFATC2, BMPR1B SHP2 signaling(N) 51 3 0.0172 IGF1R, PIK3R1, PAG1 PIP3 activates AKT 111 4 0.0172 GSK3B, FGF2, CASP9, PIK3R1 signaling(R) Role of Calcineurin- 52 3 0.0172 GSK3B, PRKCQ, NFATC2 dependent NFAT signaling in lymphocytes(N) Signaling events 52 3 0.0172 GSK3B, GRB10, PIK3R1 mediated by Stem cell factor receptor (c- Kit)(N) Endometrial cancer(K) 52 3 0.0172 GSK3B, CASP9, PIK3R1 Chemokine signaling 187 5 0.0174 GSK3B, WASL, CXCR4, PIK3R1, NFKB1 pathway(K) Signaling by SCF-KIT(R) 290 6 0.0224 GSK3B, FGF2, CASP9, GRB10, PIK3R1, NCAM1 role of pi3k subunit p85 16 2 0.0224 WASL, PIK3R1 in regulation of actin organization and cell migration(B) B cell activation(P) 59 3 0.0224 SYK, NFATC2, PTPRC Viral carcinogenesis(K) 203 5 0.0224 SYK, HDAC4, PIK3R1, EGR3, NFKB1 Epstein-Barr virus 204 5 0.0224 GSK3B, SYK, HDAC4, PIK3R1, NFKB1 infection(K) control of skeletal 17 2 0.0224 MYOD1, PIK3R1 myogenesis by hdac and calcium/calmodulin- dependent kinase (camk)(B) Signaling events 60 3 0.0225 WASL, ETS1, PIK3R1 mediated by focal adhesion kinase(N) Proteoglycans in 205 5 0.0226 FGF2, IGF1R, DCN, PIK3R1, TGFB2 cancer(K) VEGF signaling 61 3 0.0235 CASP9, PIK3R1, NFATC2 pathway(K) VEGF signaling 18 2 0.025 ETS1, CASP9 pathway(P) LPA receptor mediated 63 3 0.0251 GSK3B, PIK3R1, NFKB1 events(N) Inflammatory bowel 65 3 0.0251 RORA, TGFB2, NFKB1 disease (IBD)(K) HIF-1-alpha 65 3 0.0251 RORA, ETS1, CXCR4 transcription factor network(N) Angiogenesis(P) 66 3 0.0251 GSK3B, ETS1, CASP9 Renal cell carcinoma(K) 67 3 0.0258 ETS1, PIK3R1, TGFB2 Signaling by EGFR(R) 317 6 0.0258 GSK3B, FGF2, CASP9, PIK3R1, NCAM1, PAG1 Measles(K) 136 4 0.0258 GSK3B, PRKCQ, PIK3R1, NFKB1 C-type lectin receptors 139 4 0.0258 SYK, CARD11, NFATC2, NFKB1 (CLRs)(R) DAP12 interactions(R) 323 6 0.0258 GSK3B, FGF2, CASP9, SYK, PIK3R1, NCAM1 Insulin signaling 140 4 0.0258 GSK3B, PYGM, PIK3R1, ACACB pathway(K) AP-1 transcription 70 3 0.0258 ETS1, ELF1, NFATC2 factor network(N) CDC42 signaling 70 3 0.0258 GSK3B, WASL, PIK3R1 events(N) Adipocytokine signaling 70 3 0.0258 PRKCQ, ACACB, NFKB1 pathway(K) Melanoma(K) 71 3 0.0258 FGF2, IGF1R, PIK3R1 Ras signaling 229 5 0.0258 ETS1, FGF2, IGF1R, PIK3R1, NFKB1 pathway(K) ctcf: first multivalent 22 2 0.0264 PIK3R1, TGFB2 nuclear factor(B) Nephrin interactions(R) 22 2 0.0264 WASL, PIK3R1 Prolactin signaling 72 3 0.0266 GSK3B, PIK3R1, NFKB1 pathway(K) Breast cancer(K) 146 4 0.0283 GSK3B, FGF2, IGF1R, PIK3R1 Effects of PIP2 23 2 0.0287 PRKCQ, DGKH hydrolysis(R) Signaling events 23 2 0.0287 PIK3R1, TGFB2 mediated by the Hedgehog family(N) Glypican 1 network(N) 25 2 0.0304 FGF2, TGFBR2 Signaling by 460 7 0.0304 RORA, IL1RAP, FGF2, SYK, PIK3R1, Interleukins(R) NCAM1, NFKB1 Hippo signaling 154 4 0.0304 GSK3B, TGFBR2, TGFB2, BMPR1B pathway(K) mTOR signaling 154 4 0.0304 GSK3B, IGF1R, GRB10, PIK3R1 pathway(K) TGF-beta signaling 80 3 0.0304 TGFBR2, TGFB2, BMPR1B pathway(P) CXCR4-mediated 80 3 0.0304 CXCR4, PAG1, PTPRC signaling events(N) Signaling events 80 3 0.0304 WASL, ETS1, PIK3R1 mediated by Hepatocyte Growth Factor Receptor (c- Met)(N) Signaling events 26 2 0.0304 MYOD1, HDAC4 mediated by HDAC Class III(N) Integrin signalling 158 4 0.0304 COL4A2, COL4A1, COL13A1, PIK3R1 pathway(P) ECM-receptor 82 3 0.0304 COL4A2, COL4A1, LAMA2 interaction(K) Insulin-mediated 27 2 0.0313 GSK3B, STXBP4 glucose transport(N) Reelin signaling 28 2 0.0335 GSK3B, PIK3R1 pathway(N) IL2 signaling events 28 2 0.0335 ELF1, PIK3R1 mediated by STAT5(N) Cytokine-cytokine 265 5 0.0375 IL1RAP, TGFBR2, CXCR4, TGFB2, receptor interaction(K) BMPR1B Nectin adhesion 30 2 0.0383 PIK3R1, NECTIN3 pathway(N) Protein digestion and 90 3 0.0391 COL4A2, COL4A1, COL13A1 absorption(K) Wnt signaling 268 5 0.0392 GSK3B, MYH1, PRKCQ, NFATC2, pathway(P) BMPR1B Striated Muscle 31 2 0.0407 MYBPC1, MYL1 Contraction(R) Influenza A(K) 175 4 0.0421 GSK3B, CASP9, PIK3R1, NFKB1 Syndecan-4-mediated 32 2 0.0427 FGF2, CXCR4 signaling events(N) Netrin-mediated 32 2 0.0427 WASL, PIK3R1 signaling events(N) Propanoate 32 2 0.0427 HADHA, ACACB metabolism(K) Longevity regulating 94 3 0.0427 IGF1R, PIK3R1, NFKB1 pathway(K) Tuberculosis(K) 179 4 0.0427 CASP9, SYK, TGFB2, NFKB1 EPO signaling 33 2 0.0427 PIK3R1, NFKB1 pathway(N) HIV-1 Nef: Negative 33 2 0.0427 CASP9, NFKB1 effector of Fas and TNF- alpha(N) Inflammatory mediator 99 3 0.0427 IL1RAP, PRKCQ, PIK3R1 regulation of TRP channels(K) IL2 signaling events 35 2 0.0427 PIK3R1, NFKB1 mediated by PI3K(N) signal transduction 35 2 0.0427 IL1RAP, TGFB2 through il1r(B) Class I PI3K signaling 35 2 0.0427 GSK3B, CASP9 events mediated by Akt(N) Choline metabolism in 101 3 0.0427 WASL, DGKH, PIK3R1 cancer(K) Trk receptor signaling 36 2 0.0427 GSK3B, PIK3R1 mediated by PI3K and PLC-gamma(N) HIF-1 signaling 103 3 0.0427 IGF1R, PIK3R1, NFKB1 pathway(K) Validated 37 2 0.0427 DCN, NFATC2 transcriptional targets of API family members Fra1 and Fra2(N) IL23-mediated signaling 37 2 0.0427 PIK3R1, NFKB1 events(N) GMCSF-mediated 37 2 0.0427 SYK, PIK3R1 signaling events(N) hiv-1 defeats host- 3 1 0.0436 CXCR4 mediated resistance by cem15(B) EPHB forward 38 2 0.0449 WASL, PIK3R1 signaling(N) Signaling events 39 2 0.0472 GRB10, PIK3Rl regulated by Ret tyrosine kinase(N) Signalling by NGF(R) 421 6 0.049 GSK3B, FGF2, CASP9, PIK3R1, NCAM1, NFKB1 Signaling by FGFR3(R) 40 2 0.0495 FGF2, PIK3R1 activation of csk by 41 2 0.0518 CXCR4, PTPRC camp-dependent protein kinase inhibits signaling through the t cell receptor(B) Signaling by FGFR4(R) 41 2 0.0518 FGF2, PIK3R1 Netrin-1 signaling(R) 42 2 0.0542 WASL, PRKCQ Plasma membrane 42 2 0.0542 IGF1R, PIK3R1 estrogen receptor signaling(N) Beta3 integrin cell 43 2 0.0566 TGFBR2, COL4A1 surface interactions(N) Axon guidance 4 1 0.058 NFATC2 mediated by netrin(P) phospholipase c 4 1 0.058 PIK3R1 signaling pathway(B) Thyroid hormone 118 3 0.0601 GSK3B, CASP9, PIK3R1 signaling pathway(K) Validated 45 2 0.0616 GSK3B, STXBP4 transcriptional targets of deltaNp63 isoforms(N) Insulin Pathway(N) 45 2 0.0616 GRB10, PIK3R1 PDGFR-beta signaling 120 3 0.0628 WASL, GRB10, PAG1 pathway(N) Neurotrophin signaling 121 3 0.0642 GSK3B, PIK3R1, NFKB1 pathway(K) Platelet activation(K) 122 3 0.0656 SYK, STIM1, PIK3R1 FGF signaling 47 2 0.0667 PIK3R1, NCAM1 pathway(N) Notch-mediated 47 2 0.0667 MAML2, MYOD1 HES/HEY network(N) keratinocyte 47 2 0.0667 ETS1, PRKCQ differentiation(B) AMPK signaling 124 3 0.0667 IGF1R, PIK3R1, ACACB pathway(K) RET signaling(R) 222 4 0.0667 FGF2, GRB10, PIK3R1, NCAM1 GPVI-mediated 49 2 0.0667 SYK, PIK3R1 activation cascade(R) Signaling by FGFR1(R) 49 2 0.0667 FGF2, PIK3R1 NCAM signaling for 231 4 0.0667 FGF2, COL4A2, COL4A1, NCAM1 neurite out-growth(R) Metabolism of 233 4 0.0667 PYGM, DCN, GPC5, B3GAT2 carbohydrates(R) Hepatitis C(K) 133 3 0.0667 GSK3B, PIK3R1, NFKB1 Natural killer cell 135 3 0.0667 SYK, PIK3R1, NFATC2 mediated cytotoxicity(K) Thromboxane A2 54 2 0.0667 SYK, PRKCQ receptor signaling(N) IL2-mediated signaling 54 2 0.0667 SYK, PIK3R1 events(N) Alternative NF-kappaB 6 1 0.0667 NFKB1 pathway(N) Legionellosis(K) 55 2 0.0667 CASP9, NFKB1 Non-small cell lung 56 2 0.0667 CASP9, PIK3R1 cancer(K) Apoptosis(K) 140 3 0.0667 CASP9, PIK3R1, NFKB1 Acute myeloid 57 2 0.0667 PIK3R1, NFKB1 leukemia(K) Phospholipase D 144 3 0.0667 SYK, DGKH, PIK3R1 signaling pathway(K) Viral myocarditis(K) 59 2 0.0677 CASP9, LAMA2 Cell adhesion molecules 145 3 0.0679 NCAM1, PTPRC, NECTIN3 (CAMs)(K) MAPK signaling 255 4 0.0715 FGF2, TGFBR2, TGFB2, NFKB1 pathway(K) Signaling by Type 1 255 4 0.0715 FGF2, IGF1R, PIK3R1, NCAM1 Insulin-like Growth Factor 1 Receptor (IGF1R)(R) Gastrin-CREB signalling 376 5 0.0721 FGF2, PRKCQ, DGKH, PIK3R1, pathway via PKC and NCAM1 MAPK(R) Non-alcoholic fatty liver 151 3 0.0751 GSK3B, PIK3R1, NFKB1 disease (NAFLD)(K) IL4-mediated signaling 63 2 0.0762 ETS1, PIK3R1 events(N) Ras Pathway(P) 63 2 0.0762 GSK3B, ETS1 Ligand-independent 8 1 0.0766 CASP9 caspase activation via DCC(R) pertussis toxin- 8 1 0.0766 CXCR4 insensitive ccr5 signaling in macrophage(B) signal dependent 8 1 0.0766 MYOD1 regulation of myogenesis by corepressor mitr(B) Downstream signaling 64 2 0.0784 PRKCQ, NFATC2 in naïve CD8+ T cells(N) Longevity regulating 64 2 0.0784 IGF1R, PIK3R1 pathway - multiple species(K) Semaphorin 65 2 0.0806 GSK3B, PTPRC interactions(R) Shigellosis(K) 65 2 0.0806 WASL, NFKB1 Glioma(K) 66 2 0.0829 IGF1R, PIK3R1 Betal integrin cell 66 2 0.0829 COL4A1, LAMA2 surface interactions(N) Fcgamma receptor 159 3 0.0854 WASL, SYK, PIK3R1 (FCGR) dependent phagocytosis(R) regulators of bone 9 1 0.0859 COL4A2 mineralization(B) 5-Hydroxytryptamine 9 1 0.0859 ALDH1A2 degredation(P) p75(NTR)-mediated 69 2 0.0898 CASP9, PIK3R1 signaling(N) Fc epsilon RI signaling 70 2 0.0921 SYK, PIK3R1 pathway(K) Signaling by Insulin 277 4 0.0922 FGF2, GRB10, PIK3R1, NCAM1 receptor(R) Signaling by FGFR2(R) 71 2 0.0945 FGF2, PIK3R1 GP1b-IX-V activation 10 1 0.0952 PIK3R1 signalling(R) Leishmaniasis(K) 73 2 0.0992 TGFB2, NFKB1 Platinum drug 75 2 0.1007 CASP9, PIK3R1 resistance(K) il-7 signal 11 1 0.1007 PIK3R1 transduction(B) Alpha6 beta4 integrin- 11 1 0.1007 LAMA2 ligand interactions(N) how does salmonella 11 1 0.1007 WASL hijack a cell(B) Glucocorticoid receptor 78 2 0.1007 GSK3B, NFKB1 regulatory network(N) Bacterial invasion of 78 2 0.1007 WASL, PIK3R1 epithelial cells(K) insulin signaling 12 1 0.1007 PIK3R1 pathway(B) trka receptor signaling 12 1 0.1007 PIK3R1 pathway(B) Transcriptional 180 3 0.1007 IGF1R, TGFBR2, NFKB1 misregulation in cancer(K) C-MYB transcription 82 2 0.1007 ETS1, MYOD1 factor network(N) human cytomegalovirus 13 1 0.1007 PIK3R1 and map kinase pathways(B) Fatty acid 13 1 0.1007 ACACB biosy nthesis(K) b cell survival 13 1 0.1007 PIK3R1 pathway(B) multiple antiapoptotic 13 1 0.1007 PIK3R1 pathways from igf-1r signaling lead to bad phosphorylation(B) Visual 83 2 0.1007 PRKCQ, GPC5 phototransduction(R) Hypertrophic 83 2 0.1007 LAMA2, TGFB2 cardiomyopathy (HCM)(K) IL5-mediated signaling 14 1 0.1007 PIK3R1 events(N) Salmonella infection(K) 86 2 0.1007 WASL, NFKB1 ErbB signaling 88 2 0.1007 GSK3B, PIK3R1 pathway(K) Sumoylation by RanBP2 15 1 0.1007 HDAC4 regulates transcriptional repression(N) Dilated 90 2 0.1007 LAMA2, TGFB2 cardiomyopathy(K) FGF signaling 92 2 0.1007 FGF2, PRKCQ pathway(P) nerve growth factor 16 1 0.1007 PIK3R1 pathway (ngf)(B) y branching of actin 16 1 0.1007 WASL filaments(B) a kt signaling pathway(B) 16 1 0.1007 PIK3R1 the igf-1 receptor and 16 1 0.1007 PIK3R1 longevity(B) role of nicotinic 16 1 0.1007 PIK3R1 acetylcholine receptors in the regulation of apoptosis(B) pten dependent cell 17 1 0.1007 PIK3R1 cycle arrest and apoptosis(B) Endocrine resistance(K) 98 2 0.1007 IGF1R, PIK3R1 Progesterone-mediated 98 2 0.1007 IGF1R, PIK3R1 oocyte maturation(K) EPHA2 forward 18 1 0.1007 PIK3R1 signaling(N) Metabolism of nitric 18 1 0.1007 WASL oxide(R) Degradation of beta 18 1 0.1007 GSK3B catenin(N) mets affect on 18 1 0.1007 ETS1 macrophage differentiation(B) Phosphatidylinositol 99 2 0.1007 DGKH, PIK3R1 signaling system(K) Rap1 signaling 212 3 0.1007 FGF2, IGF1R, PIK3R1 pathway(K) Regulation of actin 214 3 0.1007 WASL, FGF2, PIK3R1 cytoskeleton(K) sprouty regulation of 19 1 0.1007 PTPRC tyrosine kinase signals(B) tgf beta signaling 19 1 0.1007 TGFB2 pathway(B) tumor suppressor arf 19 1 0.1007 PIK3R1 inhibits ribosomal biogenesis(B) Glucagon signaling 103 2 0.1007 PYGM, ACACB pathway(K) Canonical Wnt signaling 20 1 0.1007 GSK3B pathway(N) the co-stimulatory 20 1 0.1007 PIK3R1 signal during t-cell activation(B) regulation of bad 20 1 0.1007 PIK3R1 phosphorylation(B) Toll-like receptor 106 2 0.1007 PIK3R1, NFKB1 signaling pathway(K) Cardiac conduction(R) 107 2 0.1007 TRDN, STIM1 egf signaling pathway(B) 21 1 0.1007 PIK3R1 growth hormone 21 1 0.1007 PIK3R1 signaling pathway(B) E-cadherin signaling in 21 1 0.1007 PIK3R1 keratinocytes(N) igf-1 signaling 21 1 0.1007 PIK3R1 pathway(B) PDGFR-alpha signaling 21 1 0.1007 PIK3R1 pathway(N) nf-kb signaling 21 1 0.1007 NFKB1 pathway(B) TNF signaling 110 2 0.1007 PIK3R1, NFKB1 pathway(K) intrinsic prothrombin 22 1 0.1018 COL4A2 activation pathway(B) ras signaling pathway(B) 22 1 0.1018 PIK3R1 inhibition of cellular 22 1 0.1018 PIK3R1 proliferation by gleevec(B) influence of ras and rho 22 1 0.1018 PIK3R1 proteins on g1 to s transition(B) Nicotinic acetylcholine 22 1 0.1018 MYH1 receptor signaling pathway(P) alk in cardiac 23 1 0.1062 TGFB2 myocytes(B) Signaling by BMP(R) 23 1 0.1062 BMPR1B Canonical NF-kappaB 23 1 0.1062 NFKB1 pathway(N) Biosynthesis of 23 1 0.1062 HADHA unsaturated fatty acids(K) regulation of eif-4e and 23 1 0.1062 PIK3R1 p70s6 kinase(B) role of erk5 in neuronal 23 1 0.1062 PIK3R1 survival pathway(B) Mannose type O-glycan 23 1 0.1062 B3GAT2 biosynthesis(K) Leukocyte 116 2 0.11 CXCR4, PIK3R1 transendothelial migration(K) corticosteroids and 24 1 0.1106 PIK3R1 cardioprotection(B) mtor signaling 24 1 0.1106 PIK3R1 pathway(B) nfkb activation by 24 1 0.1106 TGFB2 nontypeable hemophilus influenzae(B) Hypoxia response via 24 1 0.1106 PIK3R1 HIF activation(P) transcription factor creb 24 1 0.1106 PIK3R1 and its extracellular signals(B) Myogenesis(R) 24 1 0.1106 MYOD1 Ephrin B reverse 24 1 0.1106 PIK3R1 signaling(N) skeletal muscle 24 1 0.1106 PIK3R1 hypertrophy is regulated via akt-mtor pathway(B) VEGFR3 signaling in 25 1 0.1149 PIK3R1 lymphatic endothelium(N) Fatty acid elongation(K) 25 1 0.1149 HADHA Nongenotropic 25 1 0.1149 PIK3R1 Androgen signaling(N) ras-independent 25 1 0.1149 PIK3R1 pathway in nk cell- mediated cytotoxicity(B) S1P3 pathway(N) 25 1 0.1149 CXCR4 C-MYC pathway(N) 25 1 0.1149 GSK3B fc epsilon receptor i 25 1 0.1149 PIK3R1 signaling in mast cells(B) Nephrin/Neph1 25 1 0.1149 WASL signaling in the kidney podocyte(N) tpo signaling 25 1 0.1149 PIK3R1 pathway(B) Sphingolipid signaling 120 2 0.1163 PIK3R1, NFKB1 pathway(K) S1P2 pathway(N) 26 1 0.1192 PIK3R1 IL3-mediated signaling 26 1 0.1192 PIK3R1 events(N) bioactive peptide 26 1 0.1192 PIK3R1 induced signaling pathway(B) pdgf signaling 26 1 0.1192 PIK3R1 pathway(B) PI3 kinase pathway(P) 26 1 0.1192 GSK3B ALK1 signaling 26 1 0.1192 TGFBR2 events(N) Apoptosis signaling 26 1 0.1192 PRKCQ pathway(P) activation of camp- 26 1 0.1192 CXCR4 dependent protein kinase pka(B) β-arrestins in gpcr 26 1 0.1192 CXCR4 desensitization(B) Binding and Uptake of 124 2 0.1227 COL4A2, COL4A1 Ligands by Scavenger Receptors(R) Cell cycle(K) 124 2 0.1227 GSK3B, TGFB2 Calcium signaling in the 27 1 0.1235 NFATC2 CD4+ TCR pathway(N) thrombin signaling and 27 1 0.1235 PIK3R1 protease-activated receptors(B) VEGFR1 specific 27 1 0.1235 PIK3R1 signals(N) Integrin alphaIIb beta3 27 1 0.1235 SYK signaling(R) role of β-arrestins in the 28 1 0.1278 CXCR4 activation and targeting of map kinases(B) Signaling by NOTCH2(R) 28 1 0.1278 MAML2 role of erbb2 in signal 28 1 0.1278 PIK3R1 transduction and oncology(B) Butanoate 28 1 0.1278 HADHA metabolism(K) vegf hypoxia and 28 1 0.1278 PIK3R1 angiogenesis(B) Dorso-ventral axis 28 1 0.1278 ETS1 formation(K) EGF receptor (ErbB1) 29 1 0.1321 WASL signaling pathway(N) CD40/CD40L 29 1 0.1321 NFKB1 signaling(N) erk and pi-3 kinase are 30 1 0.1363 PIK3R1 necessary for collagen binding in corneal epithelia(B) Alpha-synuclein 30 1 0.1363 SYK signaling(N) Circadian rhythm(K) 31 1 0.1405 RORA Aurora A signaling(N) 31 1 0.1405 GSK3B beta-Alanine 31 1 0.1405 HADHA metabolism(K) amb2 Integrin 31 1 0.1405 NFKB1 signaling(N) Detoxification of 31 1 0.1405 PRDX6 Reactive Oxygen Species(R) phospholipids as 31 1 0.1405 PIK3R1 signalling intermediaries(B) Mucin type O-glycan 31 1 0.1405 C1GALT1 biosynthesis(K) Antifolate resistance(K) 31 1 0.1405 NFKB1 trefoil factors initiate 31 1 0.1405 PIK3R1 mucosal healing(B) Tight junction(K) 137 2 0.1441 MYH1, PRKCQ Oncogene Induced 32 1 0.1447 ETS1 Senescence(R) HIF-2-alpha 32 1 0.1447 ETS1 transcription factor network(N) roles of β arrestin 32 1 0.1447 CXCR4 dependent recruitment of src kinases in gpcr signaling(B) FAS (CD95) signaling 32 1 0.1447 SYK pathway(N) Noncanonical Wnt 32 1 0.1447 NFATC2 signaling pathway(N) N-cadherin signaling 33 1 0.1489 PIK3R1 events(N) Apoptosis - multiple 33 1 0.1489 CASP9 species(K) FAS signaling 33 1 0.1489 CASP9 pathway(P) actions of nitric oxide in 34 1 0.153 PIK3R1 the heart(B) Signaling by Retinoic 34 1 0.153 ALDH1A2 Acid(R) Wnt signaling 143 2 0.1542 GSK3B, NFATC2 pathway(K) a6b1 and a6b4 Integrin 35 1 0.1572 PIK3R1 signaling(N) B-WICH complex 35 1 0.1572 GSK3B positively regulates rRNA expression(R) Prion diseases(K) 35 1 0.1572 NCAM1 Metabolic pathways(K) 1266 9 0.1586 PYGM, HADHA, ALDH1A2, DGKH, PON1, ACACB, B3GAT2, C1GALT1, PRDX6 Heterotrimeric G- 147 2 0.161 GSK3B, PYGM protein signaling pathway-Gi alpha and Gs alpha mediated pathway(P) Transcriptional 36 1 0.1613 FGF2 regulation of pluripotent stem cells(R) chrebp regulation by 36 1 0.1613 CXCR4 carbohydrates and camp(B) Arachidonic acid 36 1 0.1613 PON1 metabolism(R) Starch and sucrose 36 1 0.1613 PYGM metabolism(K) inactivation of gsk3 by 36 1 0.1613 PIK3R1 akt causes accumulation of b-catenin in alveolar macrophages(B) E-cadherin signaling in 36 1 0.1613 PIK3R1 the nascent adherens junction(N) Signaling by VEGF(R) 287 3 0.1645 FGF2, PIK3R1, NCAM1 Primary 37 1 0.1654 PTPRC immunodeficiency(K) Platelet Aggregation 37 1 0.1654 SYK (Plug Formation)(R) rac1 cell motility 37 1 0.1654 PIK3R1 signaling pathway(B) nfat and hypertrophy of 37 1 0.1654 PIK3R1 the heart (B) Retinoid metabolism 38 1 0.1694 GPC5 and transport(R) Pre-NOTCH Expression 38 1 0.1694 MAML2 and Processing(R) Signaling events 38 1 0.1694 HDAC4 mediated by HDAC Class II(N) Aldosterone-regulated 39 1 0.1735 PIK3R1 sodium reabsorption(K) Pyruvate metabolism(K) 39 1 0.1735 ACACB IFN-gamma pathway(N) 40 1 0.1775 PIK3R1 Tryptophan 40 1 0.1775 HADHA metabolism(K) Class I PI3K signaling 40 1 0.1775 SYK events(N) MicroRNAs in cancer(K) 299 3 0.1788 HDAC4, TGFB2, NFKB1 Intrinsic Pathway for 41 1 0.1815 CASP9 Apoptosis(R) BMP receptor 41 1 0.1815 BMPR1B signaling(N) Oxytocin signaling 159 2 0.1818 PIK3R1, NFATC2 pathway(K) Stabilization and 42 1 0.1855 IGF1R expansion of the E- cadherin adherens junction(N) Signaling by ERBB4(R) 42 1 0.1855 PIK3R1 ion channels and their 43 1 0.1895 CXCR4 functional role in vascular endothelium(B) Signaling by ERBB2(R) 43 1 0.1895 PIK3R1 PAR1-mediated 43 1 0.1895 PIK3R1 thrombin signaling events(N) LKB1 signaling events(N) 43 1 0.1895 GSK3B Fatty acid 44 1 0.1935 HADHA degradation(K) il-2 receptor beta chain 44 1 0.1935 PIK3R1 in t cell activation(B) Integrin-linked kinase 45 1 0.1974 GSK3B signaling(N) Presenilin action in 45 1 0.1974 GSK3B Notch and Wnt signaling(N) cGMP-PKG signaling 168 2 0.1977 PIK3R1, NFATC2 pathway(K) Carbohydrate digestion 46 1 0.2013 PIK3R1 and absorption(K) TNF receptor signaling 46 1 0.2013 NFKB1 pathway(N) Alzheimer's disease(K) 171 2 0.203 GSK3B, CASP9 Hedgehog signaling 47 1 0.2052 GSK3B pathway(K) IL6-mediated signaling 47 1 0.2052 PIK3R1 events(N) TGF-beta receptor 47 1 0.2052 TGFBR2 signaling(N) Apoptotic execution 47 1 0.2052 PRKCQ phase(R) Hedgehog signaling 48 1 0.2091 GSK3B events mediated by Gli proteins(N) Ceramide signaling 48 1 0.2091 NFKB1 pathway(N) Fatty acid 48 1 0.2091 HADHA metabolism(K) Posttranslational 48 1 0.2091 IGF1R regulation of adherens junction stability and dissassembly(N) Type II diabetes 48 1 0.2091 PIK3R1 mellitus(K) t cell receptor signaling 48 1 0.2091 PIK3R1 pathway(B) FoxO family signaling(N) 48 1 0.2091 FBXO32 Valine, leucine and 48 1 0.2091 HADHA isoleucine degradation(K) Notch signaling 48 1 0.2091 MAML2 pathway(K) Cocaine addiction(K) 49 1 0.213 NFKB1 Regulation of Androgen 49 1 0.213 GSK3B receptor activity(N) Malaria(K) 49 1 0.213 TGFB2 Intestinal immune 49 1 0.213 CXCR4 network for IgA production(K) Ovarian 50 1 0.2168 IGF1R steroidogenesis(K) Amyotrophic lateral 51 1 0.2207 CASP9 sclerosis (ALS)(K) Senescence-Associated 52 1 0.2245 NFKB1 Secretory Phenotype (SASP)(R) Signaling events 52 1 0.2245 PIK3R1 mediated by PTP1B(N) Caspase cascade in 52 1 0.2245 CASP9 apoptosis(N) Notch signaling 52 1 0.2245 MAML2 pathway(N) Signaling by MET(R) 52 1 0.2245 PIK3R1 Regulation of 53 1 0.2283 ACACB cholesterol biosynthesis by SREBP (SREBF)(R) Interleukin signaling 55 1 0.2358 GSK3B pathway(P) Endothelin signaling 55 1 0.2358 PRKCQ pathway(P) Basal cell carcinoma(K) 55 1 0.2358 GSK3B Pathogenic Escherichia 55 1 0.2358 WASL coli infection(K) Regulation of lipolysis in 56 1 0.2395 PIK3R1 adipocytes(K) Signaling events 56 1 0.2395 NFKB1 mediated by HDAC Class I(N) p53 pathway(N) 57 1 0.2433 GSK3B Fatty acid, 195 2 0.2461 RORA, HADHA triacylglycerol, and ketone body metabolism(R) ATF-2 transcription 58 1 0.247 TGFB2 factor network(N)

TABLE 29 Number Of Protein In Protein From GeneSet Gene Set Network FDR Nodes T cell receptor 105 6 1.54E−04 PIK3R1, CBL, PPP3CA, PPP3CC, signaling pathway(K) PLCG1, SOS1 Th17 cell 107 6 1.54E−04 PPP3CA, PPP3CC, TBX21, PLCG1, differentiation(K) IRF4, 1 LUA BCR signaling 65 5 2.02E−04 PIK3R1, PPP3CA, PPP3CC, TRAF6, pathway(N) SOS1 EPO signaling 33 4 3.11E−04 PIK3R1, CBL, PLCG1, SOS1 pathway(N) T cell activation(P) 81 5 3.49E−04 PIK3R1, PPP3CA, PPP3CC, PLCG1, SOS1 Signaling by FGFR3(R) 40 4 4.10E−04 PIK3R1, CBL, PLCG1, SOS1 Signaling by FGFR4(R) 41 4 4.10E−04 PIK3R1, CBL, PLCG1, SOS1 FGF signaling 47 4 6.22E−04 PIK3R1, CBL, PLCG1, SOS1 pathway(N) Signaling by FGFR1(R) 49 4 6.40E−04 PIK3R1, CBL, PLCG1, SOS1 TCR signaling in naïve 54 4 8.45E−04 CBL, PLCG1, TRAF6, SOS1 CD8+ T cells(N) VEGF signaling 61 4 1.10E−03 PIK3R1, PPP3CA, PPP3CC, PLCG1 pathway(K) PDGFR-alpha signaling 21 3 1.10E−03 PIK3R1, PLCG1, SOS1 pathway(N) Fc-epsilon receptor I 62 4 1.10E−03 PIK3R1, CBL, PLCG1, SOS1 signaling in mast cells(N) Renin secretion(K) 65 4 1.23E−03 PPP3CA, PPP3CC, AGT, ADRB3 TCR signaling in naïve 67 4 1.26E−03 CBL, PLCG1, TRAF6, SOS1 CD4+ T cells(N) Natural killer cell 135 5 1.26E−03 PIK3R1, PPP3CA, PPP3CC, PLCG1, mediated SOS1 cytotoxicity(K) Signaling by FGFR2(R) 71 4 1.41E−03 PIK3R1, CBL, PLCG1, SOS1 B cell receptor 73 4 1.50E−03 PIK3R1, PPP3CA, PPP3CC, SOS1 signaling pathway(K) VEGFR1 specific 27 3 1.58E−03 PIK3R1, CBL, PLCG1 signals(N) EGF receptor (ErbB1) 29 3 1.82E−03 PLCG1, GSN, SOS1 signaling pathway(N) Signaling events 80 4 1.82E−03 PIK3R1, CBL, PLCG1, SOS1 mediated by Hepatocyte Growth Factor Receptor (c- Met)(N) N-cadherin signaling 33 3 2.33E−03 PIK3R1, PLCG1, GSN events(N) ErbB signaling 88 4 2.33E−03 PIK3R1, CBL, PLCG1, SOS1 pathway(K) Th1 and Th2 cell 92 4 2.60E−03 PPP3CA, PPP3CC, TBX21, PLCG1 differentiation(K) Trk receptor signaling 36 3 2.60E−03 PIK3R1, PLCG1, SOS1 mediated by PI3K and PLC-gamma(N) Axon guidance(K) 177 5 2.60E−03 PIK3R1, PPP3CA, PPP3CC, PLCG1, BMPR1B Calcium signaling 182 5 2.96E−03 HTR2A, PPP3CA, PPP3CC, PLCG1, pathway(K) ADRB3 Glucagon signaling 103 4 3.45E−03 PPP3CA, PPP3CC, PCK1, PPARA pathway(K) Signaling by ERBB2(R) 43 3 4.02E−03 PIK3R1, PLCG1, SOS1 Insulin Pathway(N) 45 3 4.24E−03 PIK3R1, CBL, SOS1 IL6-mediated signaling 47 3 4.81E−03 PIK3R1, LMO4, SOS1 events(N) Neurotrophin 121 4 5.37E−03 PIK3R1, PLCG1, TRAF6, SOS1 signaling pathway(K) SHP2 signaling(N) 51 3 5.37E−03 PIK3R1, LMO4, SOS1 Signaling events 52 3 5.37E−03 PIK3R1, CBL, SOS1 mediated by Stem cell factor receptor (c- Kit)(N) Signaling by MET(R) 52 3 5.37E−03 PIK3R1, CBL, SOS1 Non-small cell lung 56 3 6.65E−03 PIK3R1, PLCG1, SOS1 cancer(K) Osteoclast 132 4 6.72E−03 PIK3R1, PPP3CA, PPP3CC, TRAF6 differentiation(K) Hepatitis C(K) 133 4 6.91E−03 PIK3R1, TRAF6, SOS1, PPARA Neurotrophic factor- 60 3 7.30E−03 PIK3R1, PLCG1, SOS1 mediated Trk receptor signaling(N) Signaling events 60 3 7.30E−03 PIK3R1, PLCG1, SOS1 mediated by focal adhesion kinase(N) Insulin signaling 140 4 7.47E−03 PIK3R1, CBL, PCK1, SOS1 pathway(K) Signaling pathways 142 4 7.47E−03 PIK3R1, ZFHX3, BMPR1B, BMPR1A regulating pluripotency of stem cells(K) IL4-mediated signaling 63 3 7.47E−03 PIK3R1, CBL, IRF4 events(N) Signaling events 63 3 7.47E−03 PIK3R1, CBL, PLCG1 mediated by VEGFR1 and VEGFR2(N) MAPK signaling 255 5 7.81E−03 PPP3CA, PPP3CC, NR4A1, TRAF6, pathway(K) SOS1 Glioma(K) 66 3 8.53E−03 PIK3R1, PLCG1, SOS1 Wnt signaling 268 5 8.80E−03 PPP3CA, PPP3CC, MYH1, BMPR1B, pathway(P) BMPR1A Fc epsilon receptor 405 6 8.80E−03 PIK3R1, PPP3CA, PLCG1, NR4A1, (FCERI) signaling(R) TRAF6, SOS1 Signaling by the B Cell 270 5 8.80E−03 PIK3R1, CBL, PLCG1, NR4A1, SOS1 Receptor (BCR)(R) Fc epsilon RI signaling 70 3 8.83E−03 PIK3R1, PLCG1, SOS1 pathway(K) Chronic myeloid 73 3 9.96E−03 PIK3R1, CBL, SOS1 leukemia(K) cGMP-PKG signaling 168 4 0.0114 PIK3R1, PPP3CA, PPP3CC, ADRB3 pathway(K) E-cadherin signaling in 21 2 0.0119 PIK3R1, PLCG1 keratinocytes(N) EGFR tyrosine kinase 81 3 0.0119 PIK3R1, PLCG1, SOS1 inhibitor resistance(K) EGF receptor signaling 82 3 0.0119 CBL, PLCG1, SOS1 pathway(P) Signaling by BMP(R) 23 2 0.0136 BMPR1B, BMPR1A Signaling by 460 6 0.0143 PIK3R1, CBL, IRF4, TRAF6, SOS1, Interleukins(R) IL17A Signaling by EGFR(R) 317 5 0.0152 PIK3R1, CBL, PLCG1, NR4A1, SOS1 VEGFR3 signaling in 25 2 0.016 PIK3R1, SOS1 lymphatic endothelium(N) Fc gamma R-mediated 93 3 0.0168 PIK3R1, PLCG1, GSN phagocytosis(K) IL27-mediated 26 2 0.0168 TBX21JL17A signaling events(N) RXR and RAR 26 2 0.0168 NR4A1, PPARA heterodimerization with other nuclear receptor(N) IL2 signaling events 28 2 0.0168 PIK3R1, SOS1 mediated by STAT5(N) Proteoglycans in 205 4 0.0168 PIK3R1, CBL, PLCG1, SOS1 cancer(K) Inflammatory 99 3 0.0168 PIK3R1, HTR2A, PLCG1 mediator regulation of TRP channels(K) Choline metabolism in 101 3 0.0178 PIK3R1, PLCG1, SOS1 cancer(K) Osteopontin-mediated 29 2 0.0178 PIK3R1, GSN events(N) IGF1 pathway(N) 30 2 0.019 PIK3R1, SOS1 EPHA forward 31 2 0.0203 CBL, PLCG1 signaling(N) Netrin-mediated 32 2 0.0215 PIK3R1, PLCG1 signaling events(N) toll-like receptor 32 2 0.0215 TRAF6, PPARA pathway(B) Insulin resistance(K) 109 3 0.022 PIK3R1, PCK1, PPARA Signaling by Retinoic 34 2 0.0228 PDK3, ALDH1A2 Acid(R) IL1-mediated signaling 34 2 0.0228 PIK3R1, TRAF6 events(N) Internalization of 35 2 0.0228 CBL, SOS1 ErbB1(N) IL2 signaling events 35 2 0.0228 PIK3R1, SOS1 mediated by PI3K(N) GMCSF-mediated 37 2 0.0228 PIK3R1, SOS1 signaling events(N) IL23-mediated 37 2 0.0228 PIK3R1JL17A signaling events(N) PDGFR-beta signaling 120 3 0.0229 CBL, PLCG1, SOS1 pathway(N) TCR signaling(R) 123 3 0.0246 PIK3R1, PLCG1, TRAF6 Signaling events 39 2 0.0253 PIK3R1, SOS1 regulated by Ret tyrosine kinase(N) Pathways in cancer(K) 397 5 0.0263 PIK3R1, CBL, PLCG1, TRAF6, SOS1 FOXA2 and FOXA3 40 2 0.0265 PCK1, DLK1 transcription factor networks(N) IFN-gamma 40 2 0.0265 PIK3R1, CBL pathway(N) BMP receptor 41 2 0.0278 BMPR1B, BMPR1A signaling(N) Plasma membrane 42 2 0.0291 PIK3R1, SOS1 estrogen receptor signaling(N) Signaling by ERBB4(R) 42 2 0.0291 PIK3R1, SOS1 FoxO signaling 134 3 0.031 PIK3R1, PCK1, SOS1 pathway(K) il-2 receptor beta 44 2 0.0319 PIK3R1, CBL chain in t cell activation(B) Cytokine-cytokine 265 4 0.0329 TNFRSF25, BMPR1B, IL17A, receptor BMPR1A interaction(K) Ubiquitin mediated 137 3 0.0329 UBE3A, CBL, TRAF6 proteolysis(K) Signalling by NGF(R) 421 5 0.0329 PIK3R1, PLCG1, NR4A1, TRAF6, SOS1 Calcineurin-regulated 46 2 0.0329 TBX21, IRF4 NFAT-dependent transcription in lymphocytes(N) Integrins in 47 2 0.0329 PIK3R1, CBL angiogenesis(N) Phospholipase D 144 3 0.0329 PIK3R1, PLCG1, SOS1 signaling pathway(K) Amyotrophic lateral 51 2 0.0329 PPP3CA, PPP3CC sclerosis (ALS)(K) Endometrial cancer(K) 52 2 0.0329 PIK3R1, SOS1 Signaling by SCF-KIT(R) 290 4 0.0336 PIK3R1, CBL, NR4A1, SOS1 IL2-mediated signaling 54 2 0.0353 PIK3R1, SOS1 events(N) phospholipase c 4 1 0.0362 PIK3R1 signaling pathway(B) Integrin signalling 158 3 0.0363 PIK3R1, COL5A1, SOS1 pathway(P) Oxytocin signaling 159 3 0.037 PIK3R1, PPP3CA, PPP3CC pathway(K) Regulation of lipolysis 56 2 0.0378 PIK3R1, ADRB3 in adipocytes(K) Acute myeloid 57 2 0.0391 PIK3R1, SOS1 leukemia(K) B cell activation(P) 59 2 0.0418 PPP3CA, SOS1 Coregulation of 60 2 0.0431 UBE3A, GSN Androgen receptor activity(N) basic mechanism of 5 1 0.0452 PPARA action of ppara pparb(d) and pparg and effects on gene expression(B) Opioid Signalling(R) 62 2 0.0459 PPP3CA, PPP3CC LPA receptor 63 2 0.0469 PIK3R1, PLCG1 mediated events(N) DAP12 interactions(R) 323 4 0.0469 PIK3R1, PLCG1, NR4A1, SOS1 Inflammatory bowel 65 2 0.0469 TBX21, IL17A disease (IBD)(K) Tuberculosis(K) 179 3 0.0469 PPP3CA, PPP3CC, TRAF6 Signaling by PDGF(R) 328 4 0.0469 PIK3R1, PLCG1, NR4A1, SOS1 Angiogenesis(P) 66 2 0.0469 PLCG1, SOS1 Renal cell 67 2 0.0469 PIK3R1, SOS1 carcinoma(K) Long-term 67 2 0.0469 PPP3CA, PPP3CC potentiation(K) cd40I signaling 6 1 0.0469 TRAF6 pathway(B) Amphetamine 68 2 0.0469 PPP3CA, PPP3CC addiction(K) p75(NTR)-mediated 69 2 0.0469 PIK3R1, TRAF6 signaling(N) CDC42 signaling 70 2 0.0469 PIK3R1, CBL events(N) Adipocytokine 70 2 0.0469 PCK1, PPARA signaling pathway(K) PI3K-Akt signaling 341 4 0.0469 PIK3R1, PCK1, NR4A1, SOS1 pathway(K) Inflammation 71 2 0.0469 PLCG1, SOS1 mediated by chemokine and cytokine signaling pathway(P) PPAR signaling 72 2 0.0469 PCK1, PPARA pathway(K) Prolactin signaling 72 2 0.0469 PIK3R1, SOS1 pathway(K) sumoylation as a 7 1 0.0469 UBE3A mechanism to modulate ctbp- dependent gene responses(B) Abacavir transport 7 1 0.0469 PCK1 and metabolism(R) cbI mediated ligand- 7 1 0.0469 CBL induced downregulation of egf receptors pathway(B) Viral carcinogenesis(K) 203 3 0.0469 UBE3A, PIK3R1, GSN Glucocorticoid 78 2 0.047 TBX21, NR4A1 receptor regulatory network(N) Bacterial invasion of 78 2 0.047 PIK3R1, CBL epithelial cells(K) Epstein-Barr virus 204 3 0.0475 PIK3R1, PLCG1, TRAF6 infection(K) yaci and bcma 8 1 0.048 TRAF6 stimulation of b cell immune responses(B) TGF-beta signaling 80 2 0.0492 BMPR1B, BMPR1A pathway(P) Cell surface 208 3 0.0499 PIK3R1, PLCG1, SOS1 interactions at the vascular wall(R) C-MYB transcription 82 2 0.0515 PPP3CA, ZFHX3 factor network(N) Gastrin-CREB 376 4 0.0527 PIK3R1, HTR2A, AGT, SOS1 signalling pathway via PKC and MAPK(R) Regulation of actin 214 3 0.0537 PIK3R1, GSN, SOS1 cytoskeleton(K) TGF-beta signaling 84 2 0.0538 BMPR1B, BMPR1A pathway(K) Transcriptional 84 2 0.0538 PCK1, PPARA regulation of white adipocyte differentiation(R) EGFR-dependent 9 1 0.0539 SOS1 Endothelin signaling events(N) proteasome 9 1 0.0539 UBE3A complex(B) 5-Hydroxytryptamine 9 1 0.0539 ALDH1A2 degredation(P) Small cell lung 86 2 0.0561 PIK3R1, TRAF6 cancer(K) Gap junction(K) 88 2 0.0561 HTR2A, SOS1 RET signaling(R) 222 3 0.0561 PIK3R1, PLCG1, SOS1 GP1b-IX-V activation 10 1 0.0561 PIK3R1 signalling(R) cxcr4 signaling 10 1 0.0561 PIK3R1 pathway(B) Prostate cancer(K) 89 2 0.0561 PIK3R1, SOS1 FGF signaling 92 2 0.0561 PLCG1, SOS1 pathway(P) Ras signaling 229 3 0.0561 PIK3R1, PLCG1, SOS1 pathway(K) il-7 signal 11 1 0.0561 PIK3R1 transduction(B) Metabolism of 233 3 0.0561 PCK1, GPC6, B3GAT1 carbohydrates(R) NF-kappa B signaling 95 2 0.0561 PLCG1, TRAF6 pathway(K) Endocrine 98 2 0.0561 PIK3R1, SOS1 resistance(K) insulin signaling 12 1 0.0561 PIK3R1 pathway(B) trka receptor signaling 12 1 0.0561 PIK3R1 pathway(B) Phosphatidylinositol 99 2 0.0561 PIK3R1, PLCG1 signaling system(K) Estrogen signaling 100 2 0.0561 PIK3R1, SOS1 pathway(K) AGE-RAGE signaling 101 2 0.0561 PIK3R1, PLCG1 pathway in diabetic complications(K) human 13 1 0.0561 PIK3R1 cytomegalovirus and map kinase pathways(B) Metabolism of 13 1 0.0561 AGT Angiotensinogen to Angiotensins(R) b cell survival 13 1 0.0561 PIK3R1 pathway(B) multiple antiapoptotic 13 1 0.0561 PIK3R1 pathways from igf-1r signaling lead to bad phosphorylation(B) HIF-1 signaling 103 2 0.0561 PIK3R1, PLCG1 pathway(K) Chagas disease 104 2 0.0561 PIK3R1, TRAF6 (American trypanosomiasis)(K) Toll-like receptor 106 2 0.0561 PIK3R1, TRAF6 signaling pathway(K) S1P4 pathway(N) 14 1 0.0561 PLCG1 Atypical NF-kappaB 14 1 0.0561 PIK3R1 pathway(N) IL5-mediated signaling 14 1 0.0561 PIK3R1 events(N) HTLV-I infection(K) 258 3 0.0561 PIK3R1, PPP3CA, PPP3CC Endocytosis(K) 260 3 0.0561 CBL, ADRB3, TRAF6 PIP3 activates AKT 111 2 0.0561 PIK3R1, NR4A1 signaling(R) Glutamatergic 114 2 0.0561 PPP3CA, PPP3CC synapse(K) bone remodeling(B) 16 1 0.0561 TRAF6 akt signaling 16 1 0.0561 PIK3R1 pathway(B) the igf-1 receptor and 16 1 0.0561 PIK3R1 longevity(B) nerve growth factor 16 1 0.0561 PIK3R1 pathway (ngf)(B) role of nicotinic 16 1 0.0561 PIK3R1 acetylcholine receptors in the regulation of apoptosis(B) role of pi3k subunit 16 1 0.0561 PIK3R1 p85 in regulation of actin organization and cell migration(B) Leukocyte 116 2 0.0561 PIK3R1, PLCG1 transendothelial migration(K) Toxoplasmosis(K) 118 2 0.0561 PIK3R1, TRAF6 Thyroid hormone 118 2 0.0561 PIK3R1, PLCG1 signaling pathway(K) control of skeletal 17 1 0.0561 PIK3R1 myogenesis by hdac and calcium/calmodulin- dependent kinase (camk)(B) pten dependent cell 17 1 0.0561 PIK3R1 cycle arrest and apoptosis(B) EPHA2 forward 18 1 0.0561 PIK3R1 signaling(N) S1P1 pathway(N) 18 1 0.0561 PLCG1 VEGF signaling 18 1 0.0561 PLCG1 pathway(P) regulation of pgc- 18 1 0.0561 PPARA 1a(B) AMPK signaling 124 2 0.0561 PIK3R1, PCK1 pathway(K) Oocyte meiosis(K) 124 2 0.0561 PPP3CA, PPP3CC Signaling by VEGF(R) 287 3 0.0561 PIK3R1, PLCG1, SOS1 sprouty regulation of 19 1 0.0561 CBL tyrosine kinase signals(B) tumor suppressor arf 19 1 0.0561 PIK3R1 inhibits ribosomal biogenesis(B) the co-stimulatory 20 1 0.059 PIK3R1 signal during t-cell activation(B) regulation of bad 20 1 0.059 PIK3R1 phosphorylation(B) Dopaminergic 130 2 0.0592 PPP3CA, PPP3CC synapse(K) egf signaling 21 1 0.0618 PIK3R1 pathway(B) growth hormone 21 1 0.0618 PIK3R1 signaling pathway(B) nf-kb signaling 21 1 0.0618 TRAF6 pathway(B) igf-1 signaling 21 1 0.0618 PIK3R1 pathway(B) Measles(K) 136 2 0.064 PIK3R1, TRAF6 ctcf: first multivalent 22 1 0.0647 PIK3R1 nuclear factor(B) ras signaling 22 1 0.0647 PIK3R1 pathway(B) inhibition of cellular 22 1 0.0647 PIK3R1 proliferation by gleevec(B) Nephrin 22 1 0.0647 PIK3R1 interactions(R) influence of ras and 22 1 0.0647 PIK3R1 rho proteins on g1 to s transition(B) Nicotinic acetylcholine 22 1 0.0647 MYH1 receptor signaling pathway(P) C-type lectin receptors 139 2 0.0665 PPP3CA, TRAF6 (CLRs)(R) Renin-angiotensin 23 1 0.0675 AGT system(K) Signaling by Robo 23 1 0.0675 SOS1 receptor(R) regulation of eif-4e 23 1 0.0675 PIK3R1 and p70s6 kinase(B) Canonical NF-kappaB 23 1 0.0675 TRAF6 pathway(N) Signaling events 23 1 0.0675 AGT mediated by PRL(N) role of erk5 in 23 1 0.0675 PIK3R1 neuronal survival pathway(B) Mannose type O- 23 1 0.0675 B3GAT1 glycan biosynthesis(K) Proximal tubule 23 1 0.0675 PCK1 bicarbonate reclamation(K) Signaling events 23 1 0.0675 PIK3R1 mediated by the Hedgehog family(N) Wnt signaling 143 2 0.0699 PPP3CA, PPP3CC pathway(K) corticosteroids and 24 1 0.0704 PIK3R1 cardioprotection(B) Ephrin B reverse 24 1 0.0704 PIK3R1 signaling(N) skeletal muscle 24 1 0.0704 PIK3R1 hypertrophy is regulated via akt-mtor pathway(B) mtor signaling 24 1 0.0704 PIK3R1 pathway(B) Hypoxia response via 24 1 0.0704 PIK3R1 HIF activation(P) transcription factor 24 1 0.0704 PIK3R1 creb and its extracellular signals(B) Breast cancer(K) 146 2 0.0725 PIK3R1, SOS1 fc epsilon receptor i 25 1 0.0732 PIK3R1 signaling in mast cells(B) Nephrin/Neph1 25 1 0.0732 PLCG1 signaling in the kidney podocyte(N) tpo signaling 25 1 0.0732 PIK3R1 pathway(B) Nongenotropic 25 1 0.0732 PIK3R1 Androgen signaling(N) ras-independent 25 1 0.0732 PIK3R1 pathway in nk cell- mediated cytotoxicity(B) Heterotrimeric G- 147 2 0.0733 HTR2A, ADRB3 protein signaling pathway-Gi alpha and Gs alpha mediated pathway(P) S1P2 pathway(N) 26 1 0.076 PIK3R1 IL3-mediated signaling 26 1 0.076 PIK3R1 events(N) bioactive peptide 26 1 0.076 PIK3R1 induced signaling pathway(B) β-arrestins in gpcr 26 1 0.076 PPARA desensitization(B) pdgf signaling 26 1 0.076 PIK3R1 pathway(B) Non-alcoholic fatty 151 2 0.0768 PIK3R1, PPARA liver disease (NAFLD)(K) thrombin signaling 27 1 0.0788 PIK3R1 and protease- activated receptors(B) Integrin alphaIIb beta3 27 1 0.0788 SOS1 signaling(R) p38 MAPK signaling 27 1 0.0788 TRAF6 pathway(N) Hippo signaling 154 2 0.0794 BMPR1B, BMPR1A pathway(K) mTOR signaling 154 2 0.0794 PIK3R1, SOS1 pathway(K) role of erbb2 in signal 28 1 0.0816 PIK3R1 transduction and oncology(B) IL8- and CXCR1- 28 1 0.0816 CBL mediated signaling events(N) Reelin signaling 28 1 0.0816 PIK3R1 pathway(N) Dorso-ventral axis 28 1 0.0816 SOS1 formation(K) vegf hypoxia and 28 1 0.0816 PIK3R1 angiogenesis(B) Jak-STAT signaling 158 2 0.083 PIK3R1, SOS1 pathway(K) Fcgamma receptor 159 2 0.0839 PIK3R1, PLCG1 (FCGR) dependent phagocytosis(R) CD40/CD40L 29 1 0.0844 TRAF6 signaling(N) Regulation of CDC42 30 1 0.0872 PLCG1 activity(N) Nectin adhesion 30 1 0.0872 PIK3R1 pathway(N) erk and pi-3 kinase are 30 1 0.0872 PIK3R1 necessary for collagen binding in corneal epithelia(B) Citrate cycle (TCA 30 1 0.0872 PCK1 cycle)(K) IL12 signaling 31 1 0.09 TBX21 mediated by STAT4(N) Detoxification of 31 1 0.09 PRDX6 Reactive Oxygen Species(R) phospholipids as 31 1 0.09 PIK3R1 signalling intermediaries(B) Regulation of p38- 31 1 0.09 TRAF6 alpha and p38-beta(N) trefoil factors initiate 31 1 0.09 PIK3R1 mucosal healing(B) DAG and IP3 32 1 0.0927 PLCG1 signaling(R) Alzheimer's disease(K) 171 2 0.0949 PPP3CA, PPP3CC FAS signaling 33 1 0.0955 GSN pathway(P) IL8- and CXCR2- 34 1 0.0982 CBL mediated signaling events(N) actions of nitric oxide 34 1 0.0982 PIK3R1 in the heart(B) a6b1 and a6b4 35 1 0.101 PIK3R1 Integrin signaling(N) signal transduction 35 1 0.101 TRAF6 through il1r(B) Signaling events 35 1 0.101 SOS1 mediated by TCPTP(N) inactivation of gsk3 by 36 1 0.1037 PIK3R1 akt causes accumulation of b- catenin in alveolar macrophages(B) mechanism of gene 36 1 0.1037 PPARA regulation by peroxisome proliferators via ppara(B) E-cadherin signaling in 36 1 0.1037 PIK3R1 the nascent adherens junction(N) rac1 cell motility 37 1 0.1064 PIK3R1 signaling pathway(B) ErbB2/ErbB3 signaling 37 1 0.1064 SOS1 events(N) Inositol phosphate 37 1 0.1064 PLCG1 metabolism(R) Platelet Aggregation 37 1 0.1064 SOS1 (Plug Formation)(R) nfat and hypertrophy 37 1 0.1064 PIK3R1 of the heart (B) Nucleotide-binding 38 1 0.1092 TRAF6 domain, leucine rich repeat containing receptor (NLR) signaling pathways(R) Retinoid metabolism 38 1 0.1092 GPC6 and transport(R) EPHB forward 38 1 0.1092 PIK3R1 signaling(N) Regulation of RAC1 38 1 0.1092 SOS1 activity(N) Chemokine signaling 187 2 0.1102 PIK3R1, SOS1 pathway(K) Aldosterone-regulated 39 1 0.1119 PIK3R1 sodium reabsorption(K) Pyruvate 39 1 0.1119 PCK1 metabolism(K) Class I PI3K signaling 40 1 0.1146 PLCG1 events(N) GPCR ligand 395 3 0.1171 HTR2A, AGT, ADRB3 binding(R) Intrinsic Pathway for 41 1 0.1173 PPP3CC Apoptosis(R) Fatty acid, 195 2 0.1181 AGT, PPARA triacylglycerol, and ketone body metabolism(R) Netrin-1 signaling(R) 42 1 0.12 PLCG1 PAR1-mediated 43 1 0.1226 PIK3R1 thrombin signaling events(N) cAMP signaling 200 2 0.1231 PIK3R1, PPARA pathway(K) Focal adhesion(K) 201 2 0.1241 PIK3R1, SOS1 Validated 45 1 0.128 COL5A1 transcriptional targets of deltaNp63 isoforms(N) DNA Double Strand 45 1 0.128 EYA1 Break Response(R) Carbohydrate 46 1 0.1306 PIK3R1 digestion and absorption(K) Amyloid fiber 47 1 0.1333 GSN formation(R) TGF-beta receptor 47 1 0.1333 SOS1 signaling(N) Apoptotic execution 47 1 0.1333 GSN phase(R) Rapl signaling 212 2 0.1353 PIK3R1, PLCG1 pathway(K) t cell receptor 48 1 0.1359 PIK3R1 signaling pathway(B) Type II diabetes 48 1 0.1359 PIK3R1 mellitus(K) GPVI-mediated 49 1 0.1385 PIK3R1 activation cascade(R) GPCR downstream 915 5 0.1405 PIK3R1, HTR2A, AGT, ADRB3, SOS1 signaling(R) Angiopoietin receptor 50 1 0.1412 PIK3R1 Tie2-mediated signaling(N) Vibrio cholerae 51 1 0.1438 PLCG1 infection(K) Caspase cascade in 52 1 0.1464 GSN apoptosis(N) Notch signaling 52 1 0.1464 DLK1 pathway(N) Role of Calcineurin- 52 1 0.1464 NR4A1 dependent NFAT signaling in lymphocytes(N) Mitochondrial 52 1 0.1464 PPARA biogenesis(R) Signaling events 52 1 0.1464 PIK3R1 mediated by PTPIB(N) Regulation of 53 1 0.149 PPARA cholesterol biosynthesis by SREBP (SREBF)(R) Interleukin signaling 55 1 0.1542 SOS1 pathway(P) Signaling by 59 1 0.1644 DLK1 NOTCH1(R) PI Metabolism(R) 59 1 0.1644 PIK3R1 Signaling by PTK6(R) 61 1 0.1695 CBL IL12-mediated 61 1 0.1695 TBX21 signaling events(N) Colorectal cancer(K) 62 1 0.1721 PIK3R1 Validated nuclear 62 1 0.1721 LMO4 estrogen receptor alpha network(N) Costimulation by the 63 1 0.1746 PIK3R1 CD28 family(R) Ras Pathway(P) 63 1 0.1746 SOS1 Longevity regulating 64 1 0.1771 PIK3R1 pathway - multiple species(K) Retinol metabolism(K) 65 1 0.1796 ALDH1A2 Signaling by Type 1 255 2 0.181 PIK3R1, SOS1 Insulin-like Growth Factor 1 Receptor (IGF1R)(R) Pancreatic cancer(K) 66 1 0.1821 PIK3R1 Beta1 integrin cell 66 1 0.1821 COL5A1 surface interactions(N) ISG15 antiviral 67 1 0.1846 PLCG1 mechanism(R) Circadian Clock(R) 67 1 0.1846 PPARA Central carbon 67 1 0.1846 PIK3R1 metabolism in cancer(K) Glycolysis/ 67 1 0.1846 PCK1 Gluconeogenesis(K) Interferon alpha/beta 68 1 0.1871 IRF4 signaling(R) Epithelial cell signaling 68 1 0.1871 PLCG1 in Helicobacter pylori infection(K) Regulation of 68 1 0.1871 UBE3A Telomerase(N) AP-1 transcription 70 1 0.1921 AGT factor network(N) RIG-I-like receptor 70 1 0.1921 TRAF6 signaling pathway(K) Inositol phosphate 71 1 0.1945 PLCG1 metabolism(K) Melanoma(K) 71 1 0.1945 PIK3R1 Signaling by TGF-beta 73 1 0.1994 CBL Receptor Complex(R) Leishmaniasis(K) 73 1 0.1994 TRAF6 Interferon gamma 73 1 0.1994 IRF4 signaling(R) Platinum drug 75 1 0.2043 PIK3R1 resistance(K) Signaling by Insulin 277 2 0.2053 PIK3R1, SOS1 receptor(R) Neuroactive ligand- 278 2 0.2064 HTR2A, ADRB3 receptor interaction(K) Pertussis(K) 76 1 0.2067 TRAF6 RIG-I/MDA5 mediated 77 1 0.2092 TRAF6 induction of IFN- alpha/beta pathways(R) Aldosterone synthesis 82 1 0.2212 NR4A1 and secretion(K) Visual 83 1 0.2235 GPC6 phototransduction(R) MicroRNAs in 299 2 0.2299 PLCG1, SOS1 cancer(K) Rheumatoid 90 1 0.24 IL17A arthritis(K) Salivary secretion(K) 90 1 0.24 ADRB3 Protein digestion and 90 1 0.24 COL5A1 absorption(K) GnRH signaling 92 1 0.2446 SOS1 pathway(K) Longevity regulating 94 1 0.2493 PIK3R1 pathway(K)

TABLE 30.A1 probe GeneLocus 1 ACACB_12_109146008_109150083_109185066_109187324_RR ACACB 2 ACBD6_1_180269638_180272765_180371571_180375410_RR ACBD6 3 ACBD6_1_180337907_180340909_180371571_180375410_FR ACBD6 4 ADRB3_8_37962724_37965269_37984580_37986052_FF ADRB3 5 ADRB3_8_37962724_37965269_37996522_37999233_FR ADRB3 6 ALDH1A2_15_58053198_58062371_58157807_58162832_RR ALDH1A2 7 ALDH1A2_15_58053198_58062371_58229591_58234474_RF ALDH1A2 8 ANO2_12_5767708_5775129_5922387_5930466_RR ANO2 9 ANO2_12_5872622_5877860_5922387_5930466_RR ANO2 10 B3GAT1_11_134376219_134382136_134419343_134423366_FF B3GAT1 11 B3GAT2_6_70837358_70839856_70855194_70857991_FR B3GAT2 12 B3GAT2_6_70837358_70839856_70933019_70941366_FF B3GAT2 13 BMP7_20_57274840_57277666_57290751_57294583_RF BMP7 14 C1GALT1_7_7113076_7114831_7258228_7260668_FF C1GALT1 15 CALCR_7_93553156_93563952_93593898_93597071_RF CALCR 16 CARD11_7_2966372_2970772_3066095_3073017_RR CARD11 17 CASP9_1_15526774_15533191_15569002_15572579_FR CASP9 18 CBL_11_119249760_119252653_119294588_119299643_RF CBL 19 CD36_7_80539507_80544315_80603212_80611693_FR CD36 20 CD36_7_80539507_80544315_80679651_80687690_FR CD36 21 COL13A1_10_69769669_69775141_69840301_69843474_RF COL13A1 22 COL25A1_4_109024771_109031337_109090838_109104305_RR COL25A1 23 COL25A1_4_109090838_109104305_109307411_109309712_RF COL25A1 24 COL4A2_13_110272408_110277108_110487749_110493325_FR COL4A2 25 COL5A1_9_134738485_134741113_134811418_134816113_RR COL5A1 26 CYGB_17_76511049_76513649_76555120_76557454_RF CYGB 27 CYGB_17_76533052_76534398_76555120_76557454_RF CYGB 28 CYGB_17_76555120_76557454_76593886_76595265_FF CYGB 29 CYGB_17_76555120_76557454_76593886_76595265_FR CYGB Probe_Count_Total Probe_Count_Sig HyperG_Stats FDR_HyperG 1 191 87 0.388279548 1 2 200 111 0.00091339 0.014340227 3 200 111 0.00091339 0.014340227 4 29 12 0.689607935 1 5 29 12 0.689607935 1 6 200 111 0.00091339 0.014340227 7 200 111 0.00091339 0.014340227 8 200 111 0.00091339 0.014340227 9 200 111 0.00091339 0.014340227 10 110 65 0.001249162 0.018857547 11 97 39 0.81848692 1 12 97 39 0.81848692 1 13 79 37 0.363905679 1 14 109 57 0.056359167 0.291065435 15 45 37 1.92096E−07 1.37086E−05 16 122 41 0.993686632 1 17 49 22 0.520298425 1 18 76 20 0.999603201 1 19 200 101 0.044617305 0.247106631 20 200 101 0.044617305 0.247106631 21 200 73 0.989437228 1 22 200 73 0.989437228 1 23 200 73 0.989437228 1 24 47 26 0.08460057 0.378025067 25 200 94 0.240043966 0.795082334 26 33 21 0.01973308 0.135639073 27 33 21 0.01973308 0.135639073 28 33 21 0.01973308 0.135639073 29 33 21 0.01973308 0.135639073

TABLE 30.A2 Percent_Sig logFC AveExpr t P.Value adj.P.Val B FC FC_1 LS Loop detected 1 45.55 −0.63947 −0.63947 −7.69815 3.1E−07 7.7E−06 6.84649 0.64195 −1.55775 −1 E_Trn 2 55.5 −0.40863 −0.40863 −8.71959 4.8E−08   2E−06 8.7176 0.75334 −1.32742 −1 E_Trn 3 55.5 −0.37204 −0.37204 −4.7404 0.00014 0.00085 0.65579 0.77269 −1.29418 −1 E_Trn 4 41.38 −0.43258 −0.43258 −3.39837 0.00314 0.01255 −2.26959 0.74093 −1.34965 −1 Str_Trn 5 41.38 −0.41009 −0.41009 −3.34476 0.00354 0.0137  −2.38547 0.75257 −1.32877 −1 Str_Trn 6 55.5 −0.42055 −0.42055 −8.81299 5.2E−08   5E−06 8.69347 0.74714 −1.33844 −1 Str_Trn 7 55.5 −0.38345 −0.38345 −10.298 3.5E−09 3.4E−07 11.3398 0.7666 −1.30445 −1 E_Trn 8 55.5 −0.41242 −0.41242 −5.49229   3E−05 0.00044 2.3207 0.75136 −1.33092 −1 Str_Trn 9 55.5 −0.41127 −0.41127 −5.12273 6.7E−05 0.00077 1.52446 0.75196 −1.32986 −1 Str_Trn 10 59.09 −0.41969 −0.41969 −10.1091 6.3E−09 1.1E−06 10.7772 0.74758 −1.33764 −1 Str_Trn 11 40.21 −0.37049 −0.37049 −9.68101 9.3E−09 6.4E−07 10.3519 0.77352 −1.29279 −1 E_Trn 12 40.21 0.37079 0.37079 12.5019 2.1E−10 1.1E−07 14.1122 1.29306 1.29306 1 Str_Ctrl 13 46.84 0.32369 0.32369 7.23249 7.5E−07 1.5E−05 5.94574 1.25153 1.25153 1 E_Ctrl 14 52.29 −0.55555 −0.55555 −11.0417 1.1E−09 1.6E−07 12.4709 0.6804 −1.46972 −1 E_Trn 15 82.22 0.32372 0.32372 7.81516 2.5E−07 6.6E−06 7.06808 1.25156 1.25156 1 E_Ctrl 16 33.61 −0.37618 −0.37618 −8.25898 1.1E−07 3.7E−06 7.89147 0.77047 −1.2979 −1 E_Trn 17 44.9 −0.3658 −0.3658 −7.08702 9.9E−07 1.8E−05 5.6582 0.77604 −1.28859 −1 E_Trn 18 26.32 −0.42638 −0.42638 −4.61856 0.0002  0.0017  0.42001 0.74413 −1.34385 −1 Str_Trn 19 50.5 0.36751 0.36751 3.11685 0.0057  0.01625 −2.96367 1.29012 1.29012 1 E_Ctrl 20 50.5 0.35581 0.35581 4.03354 0.00072 0.00306 −0.93652 1.27971 1.27971 1 E_Ctrl 21 36.5 −0.39187 −0.39187 −7.41112 5.3E−07 1.2E−05 6.29483 0.76214 −1.31209 −1 E_Trn 22 36.5 0.33555 0.33555 5.20733 5.1E−05 0.00037 1.69682 1.26186 1.26186 1 E_Ctrl 23 36.5 0.32915 0.32915 4.61978 0.00019 0.00106 0.38479 1.25627 1.25627 1 E_Ctrl 24 55.32 −0.36515 −0.36515 −5.22977 4.9E−05 0.00036 1.74644 0.77639 −1.28802 −1 E_Trn 25 47 −0.48145 −0.48145 −3.82029 0.00122 0.00625 −1.3463 0.71626 −1.39614 −1 Str_Trn 26 63.64 −0.47142 −0.47142 −3.45234 0.00278 0.01148 −2.15253 0.72126 −1.38647 −1 Str_Trn 27 63.64 −0.48149 −0.48149 −3.45927 0.00274 0.01134 −2.13747 0.71624 −1.39618 −1 Str_Trn 28 63.64 −0.41585 −0.41585 −2.94096 0.00862 0.02643 −3.24207 0.74958 −1.33409 −1 Str_Trn 29 63.64 −0.41368 −0.41368 −2.8539 0.01041 0.03037 −3.42204 0.75071 −1.33208 −1 Str_Trn

TABLE 30.A3 Probe sequence Probe Location 60 mer Chr Star1 End1 Start2 End2 1 TCAAGAAAAAATAATAATAATTTTTTTTTC 12 109146008 109146039 109185066 109185097 GATTCCTGCTACACATTTTGGCAGAATACT 2 ATGCAATCACCAAAAATGTTTTAATTTCTC 1 180269638 180269669 180371571 180371602 GACTCTTGGTGATCCAGGTTTCAGAACTTC 3 GGTCACCAGCACAGAATGATGATGAGGATC 1 180340878 180340909 180371571 180371602 GACTCTTGGTGATCCAGGTTTCAGAACTTC 4 CGGTCCCTCTGCCCCGGTTACCTACCCGTC 8 37965238 37965269 37986021 37986052 GACATTGGAATCACTTTCTAATCCGGGACA 5 CGGTCCCTCTGCCCCGGTTACCTACCCGTC 8 37965238 37965269 37996522 37996553 GAGGACATTCCGGCTACCCCTTCCCATCAC 6 ATTTTAAATGTGGCATTTTAGGTTTATTTC GATTTTGCATAAATTGAAAAAGCTGGAGAT 15 58053198 58053229 58157807 58157838 7 CCTTGTCTATGAAGTAAGAGATTAAATCTC GAAATAAACCTAAAATGCCACATTTAAAAT 15 58053198 58053229 58234443 58234474 8 GGGGGAAGGGCCCATGCGGACAAGTAGCTC GACTGGCCTCCCACGCCTCCTCCTTTCCTG 12 5767708 5767739 5922387 5922418 9 ATATTTAAAAAAAATTAAGATGTAATTTTC GACTGGCCTCCCACGCCTCCTCCTTTCCTG 12 5872622 5872653 5922387 5922418 10 AAACATTTCTCCTGCCCCTCCTTTTCCTTC GAGCAGCAGCGAACTGTGATTGCTGTGAGT 11 134382105 134382136 134423335 134423366 11 TTTAAAAAAGCTATGTTTCAGCATAAAATC GATTAGATGCTCTGCAGCTTCCTGAAGTGT 6 70839825 70839856 70855194 70855225 12 TTTAAAAAAGCTATGTTTCAGCATAAAATC GAGTGATTGTTTTAAGTGCTCTAGGCAAGT 6 70839825 70839856 70941335 70941366 13 TTATAGTGAGAATATATGACTTTTGTAATC GAGTTTTATCTTTATTCCCTCCCCATTGGT 20 57274840 57274871 57294552 57294583 14 AAATGTATAAGAACAGAAGAGAATTATCTC GACATGTCTGAAAAGTATTATCAGCCCTCT 7 7114800 7114831 7260637 7260668 15 TATAAAGGTGGTTAGGGACAGATTTTCATC GAATTTCACCCATGGTGGAGATATTTCACT 7 93553156 93553187 93597040 93597071 16 CTAGGAAAAAAGAATGGGAAGGAATAGATC GATATAGAATCTCAGTTATTCCTCAGGAAA 7 2966372 2966403 3066095 3066126 17 TTCAAGGAATTAAACCTAGCCCTTACTATC GATTTTAGGGTATGGATATTAGGAGCCATA 1 15533160 15533191 15569002 15569033 18 ACCGCCTCACCTCAGCTCTCCAGTGAGATC GATCCTCCCACCTAAGCTTCCCAAGTTGCT 11 119249760 119249791 119299612 119299643 19 TGCTGAAAGAAAACACAATTTATTTAAGTC GAGACACAATTAAGGTTGATACAAAAAAAG 7 80544284 80544315 80603212 80603243 20 TGCTGAAAGAAAACACAATTTATTTAAGTC GAAATTTTGGAAAAGCCCTGATTTAAGTCA 7 80544284 80544315 80679651 80679682 21 CCACACATGACTGTATATTTAAATTAATTC GATGCCCAAAGGACTGTCATAATCACTCAG 10 69769669 69769700 69843443 69843474 22 AAAACACCCTGAATTGGAAGAAAGAAACTC GAGGGATGAGTGTGTATCATCAAAGTCAAA 4 109024771 109024802 109090838 109090869 23 CATGTTTTGAAAAAACTATGCATGGATTTC GAGGGATGAGTGTGTATCATCAAAGTCAAA 4 109090838 109090869 109309681 109309712 24 TTTAGATAACCAATGTATAGTACGTTAATC GATGTGAAGTTCAAGAACTGACAAGGCTGT 13 110277077 110277108 110487749 110487780 25 CGCGGGGCCTTCTGGGCCAGGCGGGCCCTC GAAAAGCCCCACGCCCCCCCAGAGCTGCTG 9 134738485 134738516 134811418 134811449 26 CCCGGTTTCCTCATCTGTCCCTGCCCCCTC GAGACTTGACTGGGGGACAATCCACTTTGA 17 76511049 76511080 76557423 76557454 27 CCCGGTTTCCTCATCTGTCCCTGCCCCCTC GAGTCTCAGATGTGAGGGCTGGAACAGATG 17 76533052 76533083 76557423 76557454 28 CCCGGTTTCCTCATCTGTCCCTGCCCCCTC GAACAATCTTGAGCATAGAGAACCAGACCC 17 76557423 76557454 76595234 76595265 29 CCCGGTTTCCTCATCTGTCCCTGCCCCCTC GAAGTATGGAGGTAAATGCCAAAGGCTCAG 17 76557423 76557454 76593886 76593917

TABLE 30.A4 4 kb Sequence Location Chr.1 Start1.1 End1.1 Start2.1 End2.1 1 12 109146008 109150009 1.1E+08 109189067 2 1 180269638 180273639 1.8E+08 180375572 3 1 180336908 180340909 1.8E+08 180375572 4 8 37961268 37965269 3.8E+07 37986052 5 8 37961268 37965269 3.8E+07 38000523 6 15 58053198 58057199 5.8E+07 58161808 7 15 58053198 58057199 5.8E+07 58234474 8 12 5767708 5771709 5922387 5926388 9 12 5872622 5876623 5922387 5926388 10 11 134378135 134382136 1.3E+08 134423366 11 6 70835855 70839856 7.1E+07 70859195 12 6 70835855 70839856 7.1E+07 70941366 13 20 57274840 57278841 5.7E+07 57294583 14 7 7110830 7114831 7256667 7260668 15 7 93553156 93557157 9.4E+07 93597071 16 7 2966372 2970373 3066095 3070096 17 1 15529190 15533191 1.6E+07 15573003 18 11 119249760 119253761 1.2E+08 119299643 19 7 80540314 80544315 8.1E+07 80607213 20 7 80540314 80544315 8.1E+07 80683652 21 10 69769669 69773670  7E+07 69843474 22 4 109024771 109028772 1.1E+08 109094839 23 4 109090838 109094839 1.1E+08 109309712 24 13 110273107 110277108 1.1E+08 110491750 25 9 134738485 134742486 1.3E+08 134815419 26 17 76511049 76515050 7.7E+07 76557454 27 17 76533052 76537053 7.7E+07 76557454 28 17 76553453 76557454 7.7E+07 76595265 29 17 76553453 76557454 7.7E+07 76597887

TABLE 30.B1 30 DGKH_13_42011104_42015078_42235825_42240914_RR DGKH 200 99 0.078405901 0.370774891 31 DIAPH3_13_59818047_59823591_59854837_59860534_RR DIAPH3 200 91 0.389926943 1 32 DKK3_11_11956071_11968035_11984245_11993733_FR DKK3 62 37 0.010531285 0.08702167 33 DKK3_11_11956071_11968035_12010923_12019458_FF DKK3 62 37 0.010531285 0.08702167 34 DKK3_11_11956071_11968035_12010923_12019458_FR DKK3 62 37 0.010531285 0.08702167 35 DKK3_11_11956071_11968035_12048403_12051930_FR DKK3 62 37 0.010531285 0.08702167 36 DLK1_14_100687837_100692867_100749541_100751577_RF DLK1 47 28 0.025050129 0.159872776 37 DOK5_20_54466479_54470848_54572383_54577350_RF DOK5 200 107 0.005388757 0.052676227 38 EGR3_8_22681793_22682820_22737091_22739184_FF EGR3 33 16 0.375730688 1 39 EHD1_11_64868178_64874017_64914431_64916090_RF EHD1 47 8 0.999981792 1 40 EMCN_4_100525710_100532027_100732651_100738720_RR EMCN 200 121 2.82028E−06 0.000158137 41 ETS1_11_128476761_128480323_128561632_128566579_RR ETS1 200 112 0.000559145 0.010705579 42 EYA1_8_71216399_71218728_71261816_71267769_RR EYA1 139 89 2.12839E−06 0.000128522 43 FBLN2_3_13512352_13515076_13582406_13590343_RF FBLN2 193 61 0.999882361 1 44 FBXO32_8_123526212_123527874_123555254_123559065_FR FBXO32 48 27 0.06408635  0.316104415 45 FOXO1_13_40524349_40526124_40688580_40690771_RR FOXO1 199 76 0.964953638 1 46 FOXO3_6_108603215_108604436_108629992_108635481_FR FOXO3 200 94 0.240043966 0.795082334 47 FTO_16_53844989_53854574_54045378_54052319_RF FTO 200 100 0.059654823 0.302381977 48 GPC5_13_91724432_91728749_91910388_91925040_FR GPC5 200 102 0.032796361 0.195038964 49 GPC5_13_91794062_91815301_91953115_91957441_RR GPC5 200 102 0.032796361 0.195038964 50 GPC6_13_94054831_94060621_94121445_94133208_RF GPC6 200 109 0.002303017 0.026200987 51 GPC6_13_94121445_94133208_94296633_94304225_FF GPC6 200 109 0.002303017 0.026200987 52 GRB10_7_50706363_50709345_50775503_50780905_RF GRB10 200 95 0.198157163 0.697548759 53 GSN_9_121177548_121180410_121268506_121274144_FR GSN 200 80 0.902128149 1 54 GSN_9_121182946_121189020_121239116_121243347_FF GSN 200 80 0.902128149 1 55 GSN_9_121227501_121232628_121268506_121274144_FR GSN 200 80 0.902128149 1 56 GSN_9_121239116_121243347_121268506_121274144_FR GSN 200 80 0.902128149 1 57 GSN_9_121253564_121256485_121268506_121274144_RR GSN 200 80 0.902128149 1 58 HDAC9_7_18055950_18064786_18135886_18142010_RF HDAC9 200 75 0.9780749  1 59 HOXC6_12_53956382_53960014_53992251_53994278_FF HOXC6 120 71 0.000728297 0.012823129

TABLE 30.B2 30 49.5 −0.40058 −0.40058 −5.54747 2.4E−05 0.00021 2.44404 0.75755 −1.32004 −1 E_Trn 31 45.5 0.40519 0.40519 2.99897 0.00741 0.02003 −3.2148 1.32426 1.32426 1 E_Ctrl 32 59.68 −0.45219 −0.45219 −4.49834 0.00027 0.00205 0.15448 0.73093 −1.36812 −1 Str_Trn 33 59.68 −0.47444 −0.47444 −4.5659 0.00023 0.00184 0.30376 0.71975 −1.38937 −1 Str_Trn 34 59.68 −0.43473 −0.43473 −4.56246 0.00023 0.00185 0.29618 0.73983 −1.35166 −1 Str_Trn 35 59.68 −0.47393 −0.47393 −4.80125 0.00014 0.00127 0.82216 0.72 −1.38889 −1 Str_Trn 36 59.57 −0.4092 −0.4092 −4.72064 0.00016 0.00144 0.64495 0.75304 −1.32794 −1 Str_Trn 37 53.5 0.363 0.363 12.7216 1.5E−10 9.4E−08 14.389 1.28609 1.28609 1 Str_Ctrl 38 48.48 −0.37008 −0.37008 −9.47862 1.3E−08 8.1E−07 10.0177 0.77374 −1.29242 −1 E_Trn 39 17.02 −0.39552 −0.39552 −9.28016 1.8E−08   1E−06 9.68498 0.76022 −1.31541 −1 E_Trn 40 60.5 0.37461 0.37461 6.40303 4.6E−06 0.00012 4.21714 1.29649 1.29649 1 Str_Ctrl 41 56 −0.37402 −0.37402 −9.59542 1.1E−08 7.1E−07 10.2112 0.77163 −1.29596 −1 E_Trn 42 64.03 −0.42028 −0.42028 −6.88873 1.7E−06   6E−05 5.18442 0.74728 −1.33819 −1 Str_Trn 43 31.61 −0.42233 −0.42233 −8.04265 1.6E−07 4.9E−06 7.49352 0.74622 −1.34009 −1 E_Trn 44 56.25 −0.42891 −0.42891 −11.0665 1.1E−09 1.6E−07 12.5076 0.74282 −1.34621 −1 E_Trn 45 38.19 0.39325 0.39325 6.48089 3.9E−06 0.00011 4.37436 1.31335 1.31335 1 Str_Ctrl 46 47 0.36526 0.36526 6.80414 2.1E−06 6.8E−05 5.01828 1.28811 1.28811 1 Str_Ctrl 47 50 −0.43423 −0.43423 −9.87919 9.1E−09 1.4E−06 10.423 0.74009 −1.35119 −1 Str_Trn 48 51 −0.46546 −0.46546 −5.10325 6.4E−05 0.00045 1.46612 0.72424 −1.38075 −1 E_Trn 49 51 −0.36364 −0.36364 −5.17542 5.5E−05 0.00039 1.62618 0.7772 −1.28667 −1 E_Trn 50 54.5 0.52882 0.52882 2.19203 0.04152 0.08545 −4.70898 1.44274 1.44274 1 Str_Ctrl 51 54.5 0.39598 0.39598 1.79312 0.08948 0.15409 −5.38925 1.31584 1.31584 1 Str_Ctrl 52 47.5 −0.3813 −0.3813 −6.54839 2.9E−06 4.1E−05 4.56832 0.76775 −1.30252 −1 E_Trn 53 40 −0.43592 −0.43592 −4.02415 0.00077 0.00446 −0.89572 0.73922 −1.35278 −1 Str_Trn 54 40 0.38727 0.38727 10.2623   5E−09   1E−06 11.0098 1.30792 1.30792 1 Str_Ctrl 55 40 −0.48985 −0.48985 −3.90162 0.00102 0.00546 −1.16675 0.7121 −1.4043 −1 Str_Trn 56 40 −0.49057 −0.49057 −4.06412 0.00071 0.00417 −0.8072 0.71175 −1.405 −1 Str_Trn 57 40 −0.46894 −0.46894 −3.75332 0.00142 0.00697 −1.49388 0.72249 −1.3841 −1 Str_Trn 58 37.5 0.32134 0.32134 2.04678 0.05484 0.10013 −5.07725 1.24949 1.24949 1 E_Ctrl 59 59.17 −0.41983 −0.41983 −3.39948 0.00313 0.01253 −2.26719 0.74751 −1.33777 −1 Str_Trn

TABLE 30.83 30 AGAAACCACAAAGCTAGGAATTAAATTTTC 13 42011104 42011135 42235825 42235856 GAATGTTTTTCTTCCTCTTAAGTGAGATAA 31 AATACGTGGTCAATCTAAGGATTATAGTTC 13 59818047 59818078 59854837 59854868 GAAAAGATTAATGATGTATTGATGACACTT 32 GACACCTCCTCTCCCTTCCCTCCCCTTCTC 11 11968004 11968035 11984245 11984276 GAGTTATCAAAATATTTTGAGAGACAGTAT 33 GACACCTCCTCTCCCTTCCCTCCCCTTCTC 11 11968004 11968035 12019427 12019458 GATCACTTTGCAAAGCTTTGTTGGCTAGGC 34 GACACCTCCTCTCCCTTCCCTCCCCTTCTC 11 11968004 11968035 12010923 12010954 GAAGGAAAAGCCCTGGGGCCAGCTGTAGAG 35 GACACCTCCTCTCCCTTCCCTCCCCTTCTC 11 11968004 11968035 12048403 12048434 GATGGCCACATGTGGCCAGTGGCTCTCATG 36 CCGCTCTGCTATGGACCCCGGCTCGCTCTC 14 100687837 100687868 100751546 100751577 GACTTGGCCCCCAGCATGTCCTCAGCCACC 37 TTATAATTGTTACTATTGGGAAGAGGATTC 20 54466479 54466510 54577319 54577350 GACACAGAAACTAAGTTTTCAAAATAAAAA 38 GCCAAGAGGGGAAAGGACTCATGTTCTCTC 8 22682789 22682820 22739153 22739184 GACTGCCTCCTCTCCCACCTCTGCTCGGAT 39 CCACCCCTGCTGCTCTGGACCTGGTGGATC 11 64868178 64868209 64916059 64916090 GACTTTTGTTTCCTGTCATTCAAGCTGCGT 40 TTTGGTGATGAAATGAAAATAATTTATTTC 4 100525710 100525741 100732651 100732682 GAAGAGCTCCTTATTCCAGTAGAAACACAA 41 ACCATCAGAAAGCTCCATTTTCTTTTGTTC 11 128476761 128476792 128561632 128561663 GACATGATTTTATGACTGATTGGTCATAGG 42 TGTCCTTTCAAGGAAGGATTAGCATCCTTC 8 71216399 71216430 71261816 71261847 GAAAGACCTATCAGGATTTCATTTGTAATG 43 CTTGCCTAGTCTTTAATTTATTTATTTATC 3 13512352 13512383 13590312 13590343 GACATTTTTTTCTTATCAACGAGACGATGT 44 TGCAGAAAGTACTACAAAAAAAGAAGCTTC 8 123527843 123527874 123555254 123555285 GAAAATGTTGGAGATGAGAGTTTCTTCACC 45 CATGGTTTATAATCCTTTTTATACATTGTC 13 40524349 40524380 40688580 40688611 GACACTGTATTTTCACAGATCACTCTGGAG 46 AGAACTTCCTGATATATTTTTTTTCTTTTC 6 108604405 108604436 108629992 108630023 GAAGGTCTTAAAATGTTTTTAAACATGACC 47 GACTCTTAAAACAATAATATCAAACAACTC 16 53844989 53845020 54052288 54052319 GACTTGTCATTTAGTTCTTTGGGAAGCAGT 48 ACAACAGAATAGAACATATTCAATTAAATC 13 91728718 91728749 91910388 91910419 GACATAGGAATAGGTTTCAGATCCTAGTCT 49 TAATAATTTTATATAATAGAATTTTGACTC 13 91794062 91794093 91953115 91953146 GAAGTTGATGTCAAGATTTATGGCTTACAT 50 AATTAGACAACGACTATATGACTCTGTCTC 13 94054831 94054862 94133177 94133208 GACTTTAAAGCAAGTACTTCTTGTATGCTC 51 AATTAGACAACGACTATATGACTCTGTCTC 13 94133177 94133208 94304194 94304225 GAGATTGGTCTTAACACACTATTGATTATT 52 GCAAATTTTGGAGCCTAACCTCCAAAATTC 7 50706363 50706394 50780874 50780905 GAGCACAAAACTTTGTCCACATTTCTGATT 53 AAAAAGAGAAAAGCAGGTTAGCACATTGTC 9 121180379 121180410 121268506 121268537 GACCCCGCCCCCGGGATGGGGGAACTGGCC 54 CTCTATAAATTTACCAGAATATAAATTCTC 9 121188989 121189020 121243316 121243347 GAAGTGATCTCTAAATGTAATCGTAAGTTT 55 AAATTTTCAAGTGTACGATATGGTATCATC 9 121232597 121232628 121268506 121268537 GACCCCGCCCCCGGGATGGGGGAACTGGCC 56 AAACTTACGATTACATTTAGAGATCACTTC 9 121243316 121243347 121268506 121268537 GACCCCGCCCCCGGGATGGGGGAACTGGCC 57 GAGAGATGCCCACTCATACCATATAACTTC 9 121253564 121253595 121268506 121268537 GACCCCGCCCCCGGGATGGGGGAACTGGCC 58 CCACATAAAACCTTGGGTTCTTAATTTATC 7 18055950 18055981 18141979 18142010 GAAGTTGAGTTACGTGTTTAAAAAAAGAAA 59 TCATATAAATGCCCCACAGAGTGCAGCATC 12 53959983 53960014 53994247 53994278 GAACCTCGCCCCCTGCACGACCCACACAAA

TABLE 30.B4 30 13 42011104 42015105 4.2E+07 42239826 31 13 59818047 59822048  6E+07 59858838 32 11 11964034 11968035 1.2E+07 11988246 33 11 11964034 11968035 1.2E+07 12019458 34 11 11964034 11968035 1.2E+07 12014924 35 11 11964034 11968035 1.2E+07 12052404 36 14 100687837 100691838  1E+08 100751577 37 20 54466479 54470480 5.5E+07 54577350 38 8 22678819 22682820 2.3E+07 22739184 39 11 64868178 64872179 6.5E+07 64916090 40 4 100525710 100529711  1E+08 100736652 41 11 128476761 128480762 1.3E+08 128565633 42 8 71216399 71220400 7.1E+07 71265817 43 3 13512352 13516353 1.4E+07 13590343 44 8 123523873 123527874 1.2E+08 123559255 45 13 40524349 40528350 4.1E+07 40692581 46 6 108600435 108604436 1.1E+08 108633993 47 16 53844989 53848990 5.4E+07 54052319 48 13 91724748 91728749 9.2E+07 91914389 49 13 91794062 91798063 9.2E+07 91957116 50 13 94054831 94058832 9.4E+07 94133208 51 13 94129207 94133208 9.4E+07 94304225 52 7 50706363 50710364 5.1E+07 50780905 53 9 121176409 121180410 1.2E+08 121272507 54 9 121185019 121189020 1.2E+08 121243347 55 9 121228627 121232628 1.2E+08 121272507 56 9 121239346 121243347 1.2E+08 121272507 57 9 121253564 121257565 1.2E+08 121272507 58 7 18055950 18059951 1.8E+07 18142010 59 12 53956013 53960014 5.4E+07 53994278

TABLE 30.C1 60 IGF1R_15_98659065_98662585_98893484_98899517_FR IGF1R 200 106 0.008018013 0.06952724 61 IL1RAP_3_190465562_190469171_190489665_190498302_RF IL1RAP 200 89 0.502149894 1 62 IL1RAP_3_190489665_190498302_190560851_190563356_FR IL1RAP 200 89 0.502149894 1 63 KDM1A_1_23064655_23070269_23096951_23098159_FR KDM1A 47 20 0.647904687 1 64 LAMA2_6_128920996_128927003_129105731_129113311_FF LAMA2 200 150  9.1067E−19 7.14876E−16 65 LAMA2_6_129342029_129351351_129383008_129389769_FR LAMA2 200 150  9.1067E−19 7.14876E−16 66 LCK_1_32214585_32217213_32237144_32241139_RF LCK 47 19 0.750202183 1 67 LDB2_4_16489298_16494220_16535160_16542582_RR LDB2 200 108 0.003555653 0.038235451 68 LMO4_1_87315524_87318670_87343110_87349940_FF LMO4 106 81 1.57736E−11 3.09557E−09 69 LMO4_1_87315524_87318670_87355277_87360229_FR LMO4 106 81 1.57736E−11 3.09557E−09 70 MAPK10_4_86572598_86581486_86617317_86621940_FF MAPK10 200 114 0.000197862 0.005547208 71 MBNL1_3_152229500_152234786_152252961_152257281_FR MBNL1 200 91 0.389926943 1 72 MBNL1_3_152229500_152234786_152281057_152285843_FR MBNL1 200 91 0.389926943 1 73 MYBPC1_12_101527342_101530065_101646571_101655128_RF MYBPC1 186 94 0.05009075  0.263900932 74 MYH1_17_10491098_10496051_10520297_10523271_RR MYH1 103 52 0.121185055 0.485358512 75 MYH1_17_10523271_10524567_10560779_10565755_FF MYH1 103 52 0.121185055 0.485358512 76 MYO18B_22_26004818_26009467_26030914_26037279_FF MYO18B 200 73 0.989437228 1 77 NCAM1_11_113019160_113028536_113163748_113168132_FR NCAM1 200 111 0.00091339  0.014340227 78 NECTIN2_19_44815042_44816736_44827160_44828776_RR NECTIN2 47 12 0.997525539 1 79 NFKB1_4_102504137_102509238_102557818_102560252_FF NFKB1 120 73 0.00019192  0.005547208 80 NFKB1_4_102557818_102560252_102627099_102634363_FR NFKB1 120 73 0.00019192  0.005547208 81 NFKB1_4_102599188_102601960_102627099_102634363_FR NFKB1 120 73 0.00019192  0.005547208 82 NR4A1_12_51995149_51997631_52041793_52046779_RR NR4A1 47 13 0.993704481 1 83 NRXN1_2_50580957_50583587_50867546_50884047_RF NRXN1 200 110 0.00146407  0.020081546 84 NTRK2_9_84804816_84814325_84917519_84924935_FR NTRK2 200 108 0.003555653 0.038235451 85 NTRK2_9_84804816_84814325_84934592_84942655_RF NTRK2 200 108 0.003555653 0.038235451 86 PAG1_8_81007411_81018107_81069439_81070856_FR PAG1 200 126 7.40996E−08 5.81682E−06 87 PAG1_8_81007411_81018107_81126745_81129448_FR PAG1 200 126 7.40996E−08 5.81682E−06 88 PCK1_20_57527297_57530814_57551578_57557205_RR PCK1 47 27 0.047791071 0.253486424 89 PCK1_20_57527297_57530814_57570220_57572870_RR PCK1 47 27 0.047791071 0.253486424

TABLE 30.C2 60 53 −0.3995 −0.3995 −9.07793 2.6E−08 1.3E−06 9.34074 0.75812 −1.31905 −1 E_Trn 61 44.5 −0.37779 −0.37779 −9.55782 1.1E−08 7.4E−07 10.1491 0.76962 −1.29935 −1 E_Trn 62 44.5 0.34847 0.34847 11.5647 5.1E−10 9.5E−08 13.2297 1.27321 1.27321 1 E_Ctrl 63 42.55 0.45098 0.45098 11.7421 5.8E−10 2.4E−07 13.1188 1.36697 1.36697 1 Str_Ctrl 64 75 −0.38825 −0.38825 −5.36236 3.6E−05 0.00028 2.03874 0.76406 −1.3088 −1 E_Trn 65 75 −0.40794 −0.40794 −12.0446 2.6E−10 6.4E−08 13.9006 0.7537 −1.32679 −1 E_Trn 66 40.43 0.40486 0.40486 4.02911 0.00072 0.00308 −0.9465 1.32396 1.32396 1 E_Ctrl 67 54 0.33023 0.33023 5.78958 1.4E−05 0.00014 2.96874 1.25721 1.25721 1 E_Ctrl 68 76.42 −0.4253 −0.4253 −4.33423 0.00039 0.00268 −0.20873 0.74468 −1.34286 −1 Str_Trn 69 76.42 −0.45509 −0.45509 −5.12331 6.7E−05 0.00077 1.52571 0.72946 −1.37087 −1 Str_Trn 70 57 0.36948 0.36948 10.6233 2.9E−09 6.8E−07 11.5469 1.29189 1.29189 1 Str_Ctrl 71 45.5 −0.38329 −0.38329 −8.65576 5.3E−08 2.2E−06 8.60483 0.76669 −1.30431 −1 E_Trn 72 45.5 −0.42323 −0.42323 −5.76242 1.7E−05 0.00029 2.89367 0.74576 −1.34092 −1 Str_Trn 73 50.54 0.38033 0.38033 2.20515 0.04044 0.08374 −4.68518 1.30164 1.30164 1 Str_Ctrl 74 50.49 −0.41206 −0.41206 −6.14494 7.8E−06 0.00017 3.69022 0.75155 −1.33058 −1 Str_Trn 75 50.49 0.32004 0.32004 7.50348 4.4E−07   1E−05 6.47359 1.24836 1.24836 1 E_Ctrl 76 36.5 −0.36797 −0.36797 −5.42926 3.1E−05 0.00025 2.18559 0.77487 −1.29054 −1 E_Trn 77 55.5 −0.47342 −0.47342 −5.25206 4.6E−05 0.00034 1.7957 0.72026 −1.3884 −1 E_Trn 78 25.53 0.32241 0.32241 8.11688 1.4E−07 4.5E−06 7.63079 1.25042 1.25042 1 E_Ctrl 79 60.83 0.35343 0.35343 7.56553 4.8E−07 2.3E−05 6.47751 1.2776 1.2776 1 Str_Ctrl 80 60.83 −0.40158 −0.40158 −7.53437 4.2E−07 9.8E−06 6.5331 0.75703 −1.32096 −1 E_Trn 81 60.83 −0.41977 −0.41977 −16.809   8E−13 1.4E−09 19.4697 0.74754 −1.33772 −1 E_Trn 82 27.66 −0.40863 −0.40863 −6.84429 1.9E−06 6.4E−05 5.09725 0.75334 −1.32742 −1 Str_Trn 83 55 0.32026 0.32026 5.92682 1.1E−05 0.00011 3.26326 1.24856 1.24856 1 E_Ctrl 84 54 0.37084 0.37084 6.52335 3.1E−06 4.3E−05 4.5167 1.2931 1.2931 1 E_Ctrl 85 54 0.35785 0.35785 10.4559 2.7E−09 2.9E−07 11.5853 1.28152 1.28152 1 E_Ctrl 86 63 −0.38914 −0.38914 −8.8407 3.9E−08 1.8E−06 8.93009 0.76359 −1.30961 −1 E_Trn 87 63 −0.38118 −0.38118 −6.54771 2.9E−06 4.1E−05 4.56692 0.76781 −1.30241 −1 E_Trn 88 57.45 −0.4278 −0.4278 −2.90477 0.00932 0.02801 −3.31712 0.7434 −1.34518 −1 Str_Trn 89 57.45 −0.44375 −0.44375 −3.06931 0.00651 0.02147 −2.97337 0.73522 −1.36014 −1 Str_Trn

TABLE 30.C3 60 ATGAAAGAATATGATTTTTTTTTTTTACTC 15 98662554 98662585 98893484 98893515 GAGTGTAAAAGGGCTTTTACTGGTGCACAC 61 TAAATAAAATTGTCTTTTTTTGTCTTTCTC 3 190465562 190465593 190498271 190498302 GAGATTTTGAAACACCTTCAGTTTGAAGAC 62 TAAATAAAATTGTCTTTTTTTGTCTTTCTC 3 190498271 190498302 190560851 190560882 GATTACAGAGAACTAAGTACATTTTAAATC 63 GGCAGGTGGATCATTTGAGGTCAAGAGCTC 1 23070238 23070269 23096951 23096982 GACAGAGCAAGACACCATCTCCAAAAAGAA 64 TCTAAGGTATAGTTTTGGGTATAAACCATC 6 128926972 128927003 129113280 129113311 GAACATTACCCCCGATTGTTTTGGAAATTA 65 TTATTTGTTAATATCCAGTAGTATTTAATC 6 129351320 129351351 129383008 129383039 GATTGCCGTTGGCTCAAAGTAATATTTGAA 66 AAGGGCTCGGGAGCTCCCTCGGCACACCTC 1 32214585 32214616 32241108 32241139 GAGGAGTGCCAGGCATCTACTGCTCTGTCC 67 AGGAATCCATTTTCAGATCACACCCCAGTC 4 16489298 16489329 16535160 16535191 GAAAGAAAACCATTTGGATGACCGTGGAAG 68 CCCCTGGCTCACCTACACAAAATTGTGCTC 1 87318639 87318670 87349909 87349940 GACTCTACTCTTAGCCCTGCTAAATAAGTA 69 CCCCTGGCTCACCTACACAAAATTGTGCTC 1 87318639 87318670 87355277 87355308 GAATGTCTGAACAAGTGAATGAACAAATGA 70 ATTATATTAGTGCTGTAATAAAATTAAGTC 4 86581455 86581486 86621909 86621940 GACACATTTGATACTGCTTATTGGGTTATT 71 TACCTTGAAAAGCTCTTCAGTATGATTATC 3 152234755 152234786 152252961 152252992 GAAAGATTCATTTTCATGTTCCGTTTTATC 72 TACCTTGAAAAGCTCTTCAGTATGATTATC 3 152234755 152234786 152281057 152281088 GAGCTTTAGCCATTCTAGTAATTATTAAAA 73 AGATCTCACATGTAAATTAGAATAGCAGTC 12 101527342 101527373 101655097 101655128 GACTAAATATAAAGACTCAATAACCACCAT 74 TTTTCTCCCAAAGTTTATATCCTAATATTC 17 10491098 10491129 10520297 10520328 GAGGAAGGTTATATTTTTGGCTATGCATCT 75 TGTCTGTTCCAGAGTGGCCCGCAGCTCCTC 17 10524536 10524567 10565724 10565755 GAGGAGCTGGCACTCTTATACACCTCTGGG 76 TGAGTTACTGTTTTTCCTTCCTTTTGATTC 22 26009436 26009467 26037248 26037279 GAGAAGAAACCAAGAATTAGAGGGATTTAA 77 ATGAATTAATGTTTCCTAGAAAGTTGTCTC 11 113028505 113028536 113163748 113163779 GAAAGAAGAAAGTGTCAGGGTTCAACTGCC 78 GGTCAGGTCTGTGCTATGGAAAGAGCTCTC 19 44815042 44815073 44827160 44827191 GACCTCCAGTCTTTCCTCTCGCATAAATGG 79 TCTTTATGGTGTCTCTTTATATATTTACTC 4 102509207 102509238 102560221 102560252 GAGAAAGAAGTAACACACTATTGCTAATTC 80 GAATTAGCAATAGTGTGTTACTTCTTTCTC 4 102560221 102560252 102627099 102627130 GATATTTTACATGGAATCTTTCCCTTTTTA 81 TACCTTTCCATTTGTCTCCTTCCCTTCATC 4 102601929 102601960 102627099 102627130 GATATTTTACATGGAATCTTTCCCTTTTTA 82 ATCTGGCTTCACATTCCTCGGCCCTTCCTC 12 51995149 51995180 52041793 52041824 GACTCTCCCTCTGTAGGCCTCCACCATGGA 83 ATTCATTTATCTGTATTCTTAGTATGCTTC 2 50580957 50580988 50884016 50884047 GAAGGTAATATAACCTTGAAAATGTAACAA 84 CTCTTCAGGGGTGTGTGGAGTAAATAGCTC 9 84814294 84814325 84917519 84917550 GAGTTTGTCCACAGCCCTCACAGCCCTTGG 85 TAAAAAGAAACATATGAAACTTATTTTATC 9 84804816 84804847 84942624 84942655 GACCCTATAGATTTTTCAATATATGTTTAT 86 TCAGATAAGTAACTTCCTGATAATTAACTC 8 81018076 81018107 81069439 81069470 GAAGTCCAGGATTCATTATAAACACTGATA 87 TCAGATAAGTAACTTCCTGATAATTAACTC 8 81018076 81018107 81126745 81126776 GAGAAACATTTATTGGTTGTCCAATTGTTT 88 CCTCGTCGTCCCCTCTCTTCCTCGTTCCTC 20 57527297 57527328 57551578 57551609 GACAGGAAAGCATACGGAAAAAGTTAAAGA 89 CCTCGTCGTCCCCTCTCTTCCTCGTTCCTC 20 57527297 57527328 57570220 57570251 GATGCGGGACTGATTGTTACAGAACTGTTT

TABLE 30.C4 60 15 98658584 98662585 9.9E+07 98897485 61 3 190465562 190469563 1.9E+08 190498302 62 3 190494301 190498302 1.9E+08 190564852 63 1 23066268 23070269 2.3E+07 23100952 64 6 128923002 128927003 1.3E+08 129113311 65 6 129347350 129351351 1.3E+08 129387009 66 1 32214585 32218586 3.2E+07 32241139 67 4 16489298 16493299 1.7E+07 16539161 68 1 87314669 87318670 8.7E+07 87349940 69 1 87314669 87318670 8.7E+07 87359278 70 4 86577485 86581486 8.7E+07 86621940 71 3 152230785 152234786 1.5E+08 152256962 72 3 152230785 152234786 1.5E+08 152285058 73 12 101527342 101531343  1E+08 101655128 74 17 10491098 10495099 1.1E+07 10524298 75 17 10520566 10524567 1.1E+07 10565755 76 22 26005466 26009467 2.6E+07 26037279 77 11 113024535 113028536 1.1E+08 113167749 78 19 44815042 44819043 4.5E+07 44831161 79 4 102505237 102509238  1E+08 102560252 80 4 102556251 102560252  1E+08 102631100 81 4 102597959 102601960  1E+08 102631100 82 12 51995149 51999150 5.2E+07 52045794 83 2 50580957 50584958 5.1E+07 50884047 84 9 84810324 84814325 8.5E+07 84921520 85 9 84804816 84808817 8.5E+07 84942655 86 8 81014106 81018107 8.1E+07 81073440 87 8 81014106 81018107 8.1E+07 81130746 88 20 57527297 57531298 5.8E+07 57555579 89 20 57527297 57531298 5.8E+07 57574221

TABLE 30.D1 90 PCK1_20_57527297_57530814_57579772_57583521_RR PCK1 47 27 0.047791071 0.253486424 91 PCK1_20_57527297_57530814_57583521_57585923_RR PCK1 47 27 0.047791071 0.253486424 92 PDK3_X_24441637_24447950_24480152_24481252_FR PDK3 42 14 0.945004612 1 93 PDK3_X_24441637_24447950_24490440_24491541_FR PDK3 42 14 0.945004612 1 94 PHTF2_7_77800747_77805972_77956111_77960107_RR PHTF2 200 99 0.078405901 0.370774891 95 PHTF2_7_77846910_77851576_77956111_77960107_RR PHTF2 200 99 0.078405901 0.370774891 96 PIK3C3_18_42033052_42039159_42070009_42072187_RF PIK3C3 174 92 0.013813418 0.105277024 97 PIK3C3_18_42070009_42072187_42088671_42094691_FF PIK3C3 174 92 0.013813418 0.105277024 98 PIK3R1_5_68187850_68194388_68237549_68241297_FF PIK3R1 146 71 0.164362225 0.605748107 99 PIK3R1_5_68203536_68213336_68237549_68241297_FR PIK3R1 146 71 0.164362225 0.605748107 100 PLCXD2_3_111719030_111722119_111809065_111815838_RR PLCXD2 200 76 0.969310539 1 101 PPARGC1A_4_23871872_23880181_23925180_23932379_FF PPARGC1A 200 109 0.002303017 0.026200987 102 PPP3CA_4_101055418_101067369_101247819_101259416_RR PPP3CA 200 95 0.198157163 0.697548759 103 PRDX6_1_173434669_173438537_173475099_173476805_FR PRDX6 38 21 0.115306099 0.474801595 104 PRDX6_1_173434669_173438537_173477717_173485417_FR PRDX6 38 21 0.115306099 0.474801595 105 PRDX6_1_173450908_173452763_173477717_173485417_FR PRDX6 38 21 0.115306099 0.474801595 106 PRKCQ_10_6432893_6439235_6488207_6489596_FF PRKCQ 200 106 0.008018013 0.06952724 107 PTPRC_1_198595771_198598296_198659753_198666156_RF PTPRC 200 98 0.101325207 0.434758425 108 PTPRC_1_198631562_198634915_198659753_198666156_RF PTPRC 200 98 0.101325207 0.434758425 109 PTPRC_1_198659753_198666156_198697386_198704777_FR PTPRC 200 98 0.101325207 0.434758425 110 PTPRC_1_198659753_198666156_198704777_198709653_FR PTPRC 200 98 0.101325207 0.434758425 111 PTPRC_1_198659753_198666156_198721093_198724578_FF PTPRC 200 98 0.101325207 0.434758425 112 PTPRC_1_198659753_198666156_198768850_198775826_FF PTPRC 200 98 0.101325207 0.434758425 113 PYGM_11_64747174_64749438_64762879_64765587_RF PYGM 16 8 0.413940883 1 114 RGS6_14_72139099_72144564_72213251_72222544_FR RGS6 200 110 0.00146407  0.020081546 115 RORA_15_60902137_60909221_61019417_61030714_RR RORA 200 102 0.032796361 0.195038964 116 RUNX3_1_24920810_24923822_24973522_24976037_RF RUNX3 94 25 0.999868187 1 117 RYR1_19_38410632_38413089_38495982_38499305_RR RYR1 75 31 0.734667715 1 118 SGCZ_8_14631157_14642508_14656955_14664444_RF SGCZ 200 131 1.15564E−09 1.13397E−07 119 SLC35B1_17_49700402_49702340_49724264_49725934_RR SLC35B1 34 9 0.989799814 1

TABLE 30.D2 90 57.45 −0.45438 −0.45438 −3.14668 0.00549 0.01895 −2.80966 0.72983 −1.37019 −1 Str_Trn 91 57.45 −0.46711 −0.46711 −3.5423 0.00228 0.00989 −1.95661 0.72341 −1.38233 −1 Str_Trn 92 33.33 −0.51621 −0.51621 −2.91295 0.00916 0.02763 −3.30018 0.69921 −1.43019 −1 Str_Trn 93 33.33 −0.48296 −0.48296 −2.84564 0.0106  0.03078 −3.439 0.71551 −1.39761 −1 Str_Trn 94 49.5 −0.37906 −0.37906 −7.13828   9E−07 1.7E−05 5.75985 0.76894 −1.3005 −1 E_Trn 95 49.5 0.40917 0.40917 9.25447 2.5E−08 2.9E−06 9.42731 1.32792 1.32792 1 Str_Ctrl 96 52.87 0.36058 0.36058 10.1197 6.2E−09 1.1E−06 10.7935 1.28394 1.28394 1 Str_Ctrl 97 52.87 0.34906 0.34906 10.1957 4.1E−09 3.8E−07 11.1792 1.27373 1.27373 1 E_Ctrl 98 48.63 −0.40001 −0.40001 −7.21891 7.7E−07 1.5E−05 5.91903 0.75785 −1.31952 −1 E_Trn 99 48.63 −0.37383 −0.37383 −6.77717 1.8E−06 2.9E−05 5.03603 0.77173 −1.29578 −1 E_Trn 100 38 0.36966 0.36966 10.925 1.3E−09 1.8E−07 12.2976 1.29205 1.29205 1 E_Ctrl 101 54.5 0.3467 0.3467 10.5435 2.4E−09 2.6E−07 11.7202 1.27165 1.27165 1 E_Ctrl 102 47.5 −0.46232 −0.46232 −10.3242 4.5E−09 9.5E−07 11.103 0.72582 −1.37776 −1 Str_Trn 103 55.26 −0.37846 −0.37846 −6.54322   3E−06 4.2E−05 4.55767 0.76926 −1.29995 −1 E_Trn 104 55.26 −0.36712 −0.36712 −9.7319 8.6E−09   6E−07 10.4352 0.77533 −1.28977 −1 E_Trn 105 55.26 −0.43334 −0.43334 −6.62265 2.9E−06 8.8E−05 4.6585 0.74054 −1.35036 −1 Str_Trn 106 53 −0.39208 −0.39208 −8.21682 1.2E−07 3.9E−06 7.81442 0.76203 −1.31228 −1 E_Trn 107 49 0.34287 0.34287 12.2469   2E−10 5.4E−08 14.1766 1.26828 1.26828 1 E_Ctrl 108 49 0.3635 0.3635 12.1633 2.2E−10 5.8E−08 14.0631 1.28654 1.28654 1 E_Ctrl 109 49 0.32003 0.32003 11.7784 3.8E−10 7.8E−08 13.5313 1.24836 1.24836 1 E_Ctrl 110 49 0.33346 0.33346 13.2487 5.1E−11 2.3E−08 15.4853 1.26003 1.26003 1 E_Ctrl 111 49 0.3532 0.3532 12.7171   1E−10 3.8E−08 14.8025 1.27739 1.27739 1 E_Ctrl 112 49 0.33194 0.33194 12.0445 2.6E−10 6.4E−08 13.9006 1.25871 1.25871 1 E_Ctrl 113 50 −0.38806 −0.38806 −9.61961   1E−08 6.9E−07 10.2511 0.76415 −1.30864 −1 E_Trn 114 55 0.37355 0.37355 9.04986 3.5E−08 3.6E−06 9.09037 1.29554 1.29554 1 Str_Ctrl 115 51 −0.47031 −0.47031 −3.83332 0.00113 0.00442 −1.38642 0.72181 −1.38541 −1 E_Trn 116 26.6 0.36423 0.36423 10.3099 4.6E−09 9.6E−07 11.0816 1.2872 1.2872 1 Str_Ctrl 117 41.33 0.37985 0.37985 3.09107 0.0062  0.02072 −2.92745 1.3012 1.3012 1 Str_Ctrl 118 65.5 −0.39071 −0.39071 −7.31446 6.4E−07 1.3E−05 6.10649 0.76275 −1.31104 −1 E_Trn 119 26.47 −0.41926 −0.41926 −4.89024 0.00011 0.00111 1.01732 0.74781 −1.33724 −1 Str_Trn

TABLE 30.D3 90 CCTCGTCGTCCCCTCTCTTCCTCGTTCCTC 20 57527297 57527328 57579772 57579803 GAACATCTCCAAGTCAGATAATCATAACAA 91 CCTCGTCGTCCCCTCTCTTCCTCGTTCCTC 20 57527297 57527328 57583521 57583552 GAGCCTCTGTCCCAATGTCACCTCTTCAGA 92 GGGGATGGGGCCGAAATATGATTGCACTTC X 24447919 24447950 24480152 24480183 GAGTTTGTTTAGTTTTTATCTTCCCCATTT 93 GGGGATGGGGCCGAAATATGATTGCACTTC X 24447919 24447950 24490440 24490471 GAACTTCAGCACCTGACCTTTGTCATCAAC 94 AAATAATATACAAGTAGTCCAACTATTTTC 7 77800747 77800778 77956111 77956142 GAGTATTTTAGAAATTACATGAAACATGAA 95 TCAGGCTTGCAGGCTCATGCCTGCAATGTC 7 77846910 77846941 77956111 77956142 GAGTATTTTAGAAATTACATGAAACATGAA 96 ATCTATTATAATGATGCAATATTGTTAATC 18 42033052 42033083 42072156 42072187 GAGTTTTCCTTCTTAAAGAACAAACTCACC 97 ATCTATTATAATGATGCAATATTGTTAATC 18 42072156 42072187 42094660 42094691 GATTCAAAGATCAAATTAATTATTAAAGCT 98 CTGAGTCTTCATTACCAAAAAAAAAAGTTC 5 68194357 68194388 68241266 68241297 GAACATGCACTGGGGTTTTACTAAAACTAT 99 CGTTGCAAATTGTACATCTTCTGCTATTTC 5 68213305 68213336 68237549 68237580 GAATGCGAAGTTGAGAAATTTTACTTATTT 100 TACTTTTTTCATATGGATATACAGTTATTC 3 111719030 111719061 111809065 111809096 GAGGAGGAATAGTCACATAAATAAATTATT 101 TACATGAATATACAGTCTTGTATTGTTTTC 4 23880150 23880181 23932348 23932379 GATCTATAGAATGGAAGGATAGCATTAGCT 102 TCTTTGTTTCCTGTTTCCACTTCTTATTTC 4 101055418 101055449 101247819 101247850 GATATTTATTGAGTGCTACTATATATATGC 103 ACTGTATCTTTTGCTTATTTTCTATACTTC 1 173438506 173438537 173475099 173475130 GAGGCATAGAACCTTTCCTTAAACTTATTT 104 ACTGTATCTTTTGCTTATTTTCTATACTTC 1 173438506 173438537 173477717 173477748 GATCCCTCCTGGCCTCCCCGCCTCCGGCGT 105 TAATGCTGGAGCAAGACAAAGATAGACTTC 1 173452732 173452763 173477717 173477748 GATCCCTCCTGGCCTCCCCGCCTCCGGCGT 106 TTCCACCTGTAATACTGTGCCTGTATTCTC 10 6439204 6439235 6489565 6489596 GACTCTTCTCGCCCTCTTCTCCAGCTCTCT 107 AGAGGCTGAGGTGAAAAGATTGTTTGAGTC 1 198595771 198595802 198666125 198666156 GAAGATCATTGTCTCATTTTTTTACTTGTT 108 AGAGGCTGAGGTGAAAAGATTGTTTGAGTC 1 198631562 198631593 198666125 198666156 GACAAATGTTATACATGGCTTGTAACACTG 109 AGAGGCTGAGGTGAAAAGATTGTTTGAGTC 1 198666125 198666156 198697386 198697417 GACAACCCAATTTTGTTATTTGAGTTTCTT 110 AGAGGCTGAGGTGAAAAGATTGTTTGAGTC 1 198666125 198666156 198704777 198704808 GAATTCAATTTTACTGCAAACCTCAGCATC 111 AGAGGCTGAGGTGAAAAGATTGTTTGAGTC 1 198666125 198666156 198724547 198724578 GATACACTGAACAAGTGCCAGAGCAGAATA 112 AGAGGCTGAGGTGAAAAGATTGTTTGAGTC 1 198666125 198666156 198775795 198775826 GAGTCACATGATCAAGCGCTCATTTCTGTT 113 GAGGAGAGAAAGAAGACAAAGAAGACACTC 11 64747174 64747205 64765556 64765587 GATCTGCCCTGCGGCCCCACCTGAGTGATT 114 AATGGCATTCTCCATTTATTCGTATTTATC 14 72144533 72144564 72213251 72213282 GAGACTTTCTATGAAAGCTTTTTTGATGTT 115 GGCTGAAGAATGGAATTGAAGTAGAAAATC 15 60902137 60902168 61019417 61019448 GATGATTATCAAGTATATACCAAACATTAT 116 CTTAATTTTTTTTCTTTGAATGCCTCTATC 1 24920810 24920841 24976006 24976037 GACAGTCTTCTCTCTACTTTCTACAGTGAA 117 GGTGGGAGGATCACTTGAGGTCAGAAGTTC 19 38410632 38410663 38495982 38496013 GATCTCCTGACCTCAAGTGATCCTCTAGCT 118 ATGAAAGAAATACCAATATTTGTTTAATTC 8 14631157 14631188 14664413 14664444 GAATCTCCAACACGTTATTTACCACTGGGA 119 TGGTGGCTGAGTCCTGGCACAGCCACTGTC 17 49700402 49700433 49724264 49724295 GAAGCTGGGCCCCGCACCCCCCACACAAAC

TABLE 30.D4 90 20 57527297 57531298 5.8E+07 57583773 91 20 57527297 57531298 5.8E+07 57587522 92 X 24443949 24447950 2.4E+07 24484153 93 X 24443949 24447950 2.4E+07 24494441 94 7 77800747 77804748 7.8E+07 77960112 95 7 77846910 77850911 7.8E+07 77960112 96 18 42033052 42037053 4.2E+07 42072187 97 18 42068186 42072187 4.2E+07 42094691 98 5 68190387 68194388 6.8E+07 68241297 99 5 68209335 68213336 6.8E+07 68241550 100 3 111719030 111723031 1.1E+08 111813066 101 4 23876180 23880181 2.4E+07 23932379 102 4 101055418 101059419  1E+08 101251820 103 1 173434536 173438537 1.7E+08 173479100 104 1 173434536 173438537 1.7E+08 173481718 105 1 173448762 173452763 1.7E+08 173481718 106 10 6435234 6439235 6485595 6489596 107 1 198595771 198599772  2E+08 198666156 108 1 198631562 198635563  2E+08 198666156 109 1 198662155 198666156  2E+08 198701387 110 1 198662155 198666156  2E+08 198708778 111 1 198662155 198666156  2E+08 198724578 112 1 198662155 198666156  2E+08 198775826 113 11 64747174 64751175 6.5E+07 64765587 114 14 72140563 72144564 7.2E+07 72217252 115 15 60902137 60906138 6.1E+07 61023418 116 1 24920810 24924811 2.5E+07 24976037 117 19 38410632 38414633 3.8E+07 38499983 118 8 14631157 14635158 1.5E+07 14664444 119 17 49700402 49704403  5E+07 49728265

TABLE 30.E1 120 SLC35D1_1_66998822_67004850_67070417_67074223_FR SLC35D1 83 35 0.689428445 1 121 SMAD7_18_48917335_48920290_48969505_48974578_RF SMAD7 49 21 0.632626918 1 122 STIM1_11_4071215_4074242_4084365_4091420_FR STIM1 200 71 0.99529685  1 123 STK39_2_167959346_167965882_168109573_168114525_FF STK39 200 95 0.198157163 0.697548759 124 STK39_2_168057412_168062336_168109573_168114525_FF STK39 200 95 0.198157163 0.697548759 125 STXBP4_17_55035186_55042800_55142272_55149288_FR STXBP4 178 72 0.865724188 1 126 SULF2_20_47663998_47665865_47797013_47801718_FR SULF2 200 95 0.198157163 0.697548759 127 SYK_9_90789107_90793598_90876350_90879196_RF SYK 189 111 4.46333E−05 0.001946506 128 SYK_9_90816328_90822228_90832284_90836084_RR SYK 189 111 4.46333E−05 0.001946506 129 SYK_9_90816328_90822228_90836573_90843345_FR SYK 189 111 4.46333E−05 0.001946506 130 SYK_9_90816328_90822228_90836573_90843345_RR SYK 189 111 4.46333E−05 0.001946506 131 SYK_9_90816328_90822228_90872966_90875740_RR SYK 189 111 4.46333E−05 0.001946506 132 TBX21_17_47685438_47687129_47704291_47707744_FR TBX21 2 0 1       1 133 TGFB2_1_218317687_218325587_218386401_218389011_FR TGFB2 132 81 5.75498E−05 0.002258828 134 TGFBR2_3_30563062_30565548_30608158_30611268_FF TGFBR2 200 116  6.4811E−05 0.002312575 135 TGFBR2_3_30566144_30567439_30633318_30636860_RR TGFBR2 200 116  6.4811E−05 0.002312575 136 TGFBR2_3_30566144_30567439_30694718_30698514_RR TGFBR2 200 116  6.4811E−05 0.002312575 137 TGFBR2_3_30641481_30645057_30688470_30694718_FF TGFBR2 200 116  6.4811E−05 0.002312575 138 THADA_2_43260154_43263093_43324949_43335508_FF THADA 200 116  6.4811E−05 0.002312575 139 THADA_2_43260154_43263093_43415062_43421910_FF THADA 200 116  6.4811E−05 0.002312575 140 THNSL2_2_88139809_88146295_88161717_88164554_FF THNSL2 29 22 0.000554527 0.010705579 141 THNSL2_2_88139809_88146295_88161717_88164554_FR THNSL2 29 22 0.000554527 0.010705579 142 TLR2_4_153659613_153661830_153693586_153700349_RF TLR2 35 27 7.79458E−05 0.002581174 143 TNFRSF25_1_6481328_6484248_6494588_6498048_FR TNFRSF25 23 9 0.758494992 1 144 TTN_2_178554164_178555670_178788193_178796485_FR TTN 200 105 0.011714369 0.093834484 145 UACA_15_70715123_70719636_70780754_70784668_RF UACA 171 86 0.066058747 0.322087682 146 WASL_7_123664155_123666896_123763390_123768284_RF WASL 117 46 0.880312179 1 147 ZEB1_10_31273317_31275631_31437913_31439545_RF ZEB1 181 122 2.83212E−10 3.70535E−08 148 ZEB1_10_31273317_31275631_31507470_31524442_FF ZEB1 181 122 2.83212E−10 3.70535E−08 149 ZEB1_10_31437913_31439545_31458964_31462037_FR ZEB1 181 122 2.83212E−10 3.70535E−08

TABLE 30.E2 120 42.17 0.32021 0.32021 6.5647 2.8E−06   4E−05 4.60189 1.24851 1.24851 1 E_Ctrl 121 42.86 0.40277 0.40277 2.5496 0.01993 0.04923 −4.03372 1.32205 1.32205 1 Str_Ctrl 122 35.5 −0.38567 −0.38567 −6.19747 6.1E−06 7.2E−05 3.83751 0.76542 −1.30647 −1 E_Trn 123 47.5 −0.38658 −0.38658 −6.41859 3.8E−06 5.1E−05 4.29985 0.76494 −1.30729 −1 E_Trn 124 47.5 −0.38862 −0.38862 −6.08691 7.6E−06 8.6E−05 3.60402 0.76386 −1.30914 −1 E_Trn 125 40.45 −0.39909 −0.39909 −8.20964 1.2E−07   4E−06 7.80127 0.75834 −1.31868 −1 E_Trn 126 47.5 −0.41472 −0.41472 −4.62876 0.0002  0.00167 0.44251 0.75016 −1.33304 −1 Str_Trn 127 58.73 −0.40056 −0.40056 −15.082 5.4E−12 5.3E−09 17.6554 0.75756 −1.32002 −1 E_Trn 128 58.73 0.45488 0.45488 6.89229 1.5E−06 2.5E−05 5.26872 1.37067 1.37067 1 E_Ctrl 129 58.73 −0.41655 −0.41655 −6.92127 1.4E−06 2.3E−05 5.32701 0.74922 −1.33473 −1 E_Trn 130 58.73 0.43262 0.43262 6.95618 1.3E−06 2.2E−05 5.39709 1.34968 1.34968 1 E_Ctrl 131 58.73 0.49185 0.49185 7.3328 6.2E−07 1.3E−05 6.14231 1.40625 1.40625 1 E_Ctrl 132 0 −0.40849 −0.40849 −1.91206 0.07163 0.12978 −5.19571 0.75341 −1.32729 −1 Str_Trn 133 61.36 −0.42784 −0.42784 −9.6318   1E−08 6.8E−07 10.2712 0.74338 −1.34521 −1 E_Trn 134 58 −0.38523 −0.38523 −10.9424 1.3E−09 1.8E−07 12.3234 0.76566 −1.30607 −1 E_Trn 135 58 0.62646 0.62646 4.01916 0.00078 0.00449 −0.90676 1.54377 1.54377 1 Str_Ctrl 136 58 0.71377 0.71377 5.02096 8.4E−05 0.00091 1.30298 1.64008 1.64008 1 Str_Ctrl 137 58 −0.38301 −0.38301 −6.46184 3.5E−06 4.7E−05 4.38955 0.76684 −1.30406 −1 E_Trn 138 58 −0.44624 −0.44624 −2.33673 0.03099 0.06849 −4.44221 0.73395 −1.36248 −1 Str_Trn 139 58 −0.49656 −0.49656 −2.6351 0.01664 0.04305 −3.86485 0.7088 −1.41084 −1 Str_Trn 140 75.86 0.33309 0.33309 6.66784 2.3E−06 3.4E−05 4.81339 1.25971 1.25971 1 E_Ctrl 141 75.86 0.3483 0.3483 5.48285 2.8E−05 0.00023 2.30294 1.27306 1.27306 1 E_Ctrl 142 77.14 0.37061 0.37061 12.6902 1.6E−10 9.4E−08 14.3497 1.2929 1.2929 1 Str_Ctrl 143 39.13 −0.421 −0.421 −2.51835 0.02128 0.05168 −4.09478 0.74691 −1.33885 −1 Str_Trn 144 52.5 0.32765 0.32765 14.3916 1.2E−11 8.6E−09 16.8699 1.25496 1.25496 1 E_Ctrl 145 50.29 −0.45244 −0.45244 −6.64511 2.4E−06 3.5E−05 4.76692 0.7308 −1.36836 −1 E_Trn 146 39.32 −0.54064 −0.54064 −8.60372 5.8E−08 2.4E−06 8.51248 0.68746 −1.45462 −1 E_Trn 147 67.4 0.3798 0.3798 3.26917 0.00406 0.01232 −2.63478 1.30116 1.30116 1 E_Ctrl 148 67.4 0.3414 0.3414 8.35815   9E−08 3.2E−06 8.07177 1.26699 1.26699 1 E_Ctrl 149 67.4 0.35465 0.35465 3.41727 0.00291 0.00948 −2.31101 1.27867 1.27867 1 E_Ctrl

TABLE 30.E3 120 TAAATTTTTACTTGTATTTTTTTGCATTTC 1 67004819 67004850 67070417 67070448 GAGTACTGTTTCCTTATTGGTCTTCTATAT 121 TATGAATCCCTAAATGTCACACATCAAGTC 18 48917335 48917366 48974547 48974578 GAATTATATAAGATACCCTGAAATTTAAGG 122 CTTGTTATGATTTTAGTATGAGATAGTTTC 11 4074211 4074242 4084365 4084396 GAGACAGAATTTATTTGTAATTTTATCAAT 123 TCTGCGCAAGTTTTAATTTTCTCTAAGGTC 2 167965851 167965882 168114494 168114525 GATTTCCCCACCTTCCCAACCTCCAAGGGT 124 TAAAATATAAATGAAAGAAGTACCTCGTTC 2 168062305 168062336 168114494 168114525 GATTTCCCCACCTTCCCAACCTCCAAGGGT 125 TTTCATTTAGTTAAAACCAGATACATAATC 17 55042769 55042800 55142272 55142303 GAGAGCACAAAGGGGAATCCCAACAGACTC 126 CCTCTCCCGCTCTCCACTCACCTCGTGGTC 20 47665834 47665865 47797013 47797044 GAAGTGTTGTCCCTGGACTGGCAGCATCTG 127 AAATTATGTTTCATGGAATGATCAGGAATC 9 90789107 90789138 90879165 90879196 GAAACTCTCTCCAATGAAACAATTCTTTGA 128 ATGACTGTGGAAGGTTCTGATGTCTCTGTC 9 90816328 90816359 90832284 90832315 GATGAAATGGAGAGAGGAGAAAGAAAAGAA 129 TTTTACTGTTTTTGTAAGAGATATGTTTTC 9 90822197 90822228 90836573 90836604 GAGAGTTGCAAGTACCTGCCTAAATCACTG 130 ATGACTGTGGAAGGTTCTGATGTCTCTGTC 9 90816328 90816359 90836573 90836604 GAGAGTTGCAAGTACCTGCCTAAATCACTG 131 ATGACTGTGGAAGGTTCTGATGTCTCTGTC 9 90816328 90816359 90872966 90872997 GACATCATTTTTACAAATAAGACCAGATGT 132 GAGAGAGCGCCTGACATATAGTAGACCTTC 17 47687098 47687129 47704291 47704322 GAGGAGAGAGAAGGGGCTCAAGGCGCCCGA 133 AATATTGCTACTGGAAAATCTGAATCTTTC 1 218325556 218325587 218386401 218386432 GAAGAAAGCCCTTTGTAAGTTGTTTTCAAA 134 TTAATTTTCAAAAATTCATTTCCAACATTC 3 30565517 30565548 30611237 30611268 GACCTCAGTTGCATTAGATACAGTAGGATG 135 AACTATGTGACTTTTAGCTATACGAGTTTC 3 30566144 30566175 30633318 30633349 GATAAATCATGATCATGGTAATAATAATTA 136 AACTATGTGACTTTTAGCTATACGAGTTTC 3 30566144 30566175 30694718 30694749 GACTGGGTTCTAAATAGTTAATGTCATAGT 137 TTTCCCTTTCCTTTAGACCATCTCTCTTTC 3 30645026 30645057 30694687 30694718 GATAACTAAGAAGAAGCTACAGAATCTCTC 138 GTTTGTCCTTCTCCCACCCTACCCCAACTC 2 43263062 43263093 43335477 43335508 GAATCATTGACCTAGAATTTTAGAACTGGA 139 GTTTGTCCTTCTCCCACCCTACCCCAACTC 2 43263062 43263093 43421879 43421910 GATCTCTCAAAGAAAAGAAGTTGGGATGCC 140 TATCAAGTTAAACATTCAGACGTCTAGGTC 2 88146264 88146295 88164523 88164554 GAGTAGTATTTAGCTTTCTTCCTTTCTAAC 141 TATCAAGTTAAACATTCAGACGTCTAGGTC 2 88146264 88146295 88161717 88161748 GACTTGAAGTTCACCTAAAGTTTTCCAGTC 142 TAAAACTATTTTAAATGTTTTTAAAGTATC 4 153659613 153659644 153700318 153700349 GATGTGTACTTTGACATCTGTGATGATGAT 143 GCACCCCACCCTGGATCCCTTGAAAGCCTC 1 6484217 6484248 6494588 6494619 GACAATGTTATTCTTTGTTTCTCTTACCAA 144 TTGGAATTATCAAGAAAGATAACTAAATTC 2 178555639 178555670 178788193 178788224 GAAAAAGATGTATTTGTTTTTGTTTAATAG 145 ATAGTATAGAATGACAGCATGCTGGTTATC 15 70715123 70715154 70784637 70784668 GACAAGAGTTCTTAAAAAGCCTAAATGTCA 146 GCCATTATTAAAATAAAAACCAAACAATTC 7 123664155 123664186 123768253 123768284 GATAAATGTGTATTGAAGUTTTTCCCTTT 147 GTGTTCTAGATGAGGGGAACAGTGGTGATC 10 31273317 31273348 31439514 31439545 GAAGTATACTAACTGAAGGAGAATAAAAAA 148 ATTCCACAAATATTTGTGAGCACCATCTTC 10 31275600 31275631 31524411 31524442 GAGCTCATTAGTTCAAGACCAGCCTGGGCA 149 GTGTTCTAGATGAGGGGAACAGTGGTGATC 10 31439514 31439545 31458964 31458995 GAAAATGCATTTAATATACTTAACCTATCA

TABLE 30.E4 120 1 67000849 67004850 6.7E+07 67074418 121 18 48917335 48921336 4.9E+07 48974578 122 11 4070241 4074242 4084365 4088366 123 2 167961881 167965882 1.7E+08 168114525 124 2 168058335 168062336 1.7E+08 168114525 125 17 55038799 55042800 5.5E+07 55146273 126 20 47661864 47665865 4.8E+07 47801014 127 9 90789107 90793108 9.1E+07 90879196 128 9 90816328 90820329 9.1E+07 90836285 129 9 90818227 90822228 9.1E+07 90840574 130 9 90816328 90820329 9.1E+07 90840574 131 9 90816328 90820329 9.1E+07 90876967 132 17 47683128 47687129 4.8E+07 47708292 133 1 218321586 218325587 2.2E+08 218390402 134 3 30561547 30565548 3.1E+07 30611268 135 3 30566144 30570145 3.1E+07 30637319 136 3 30566144 30570145 3.1E+07 30698719 137 3 30641056 30645057 3.1E+07 30694718 138 2 43259092 43263093 4.3E+07 43335508 139 2 43259092 43263093 4.3E+07 43421910 140 2 88142294 88146295 8.8E+07 88164554 141 2 88142294 88146295 8.8E+07 88165718 142 4 153659613 153663614 1.5E+08 153700349 143 1 6480247 6484248 6494588 6498589 144 2 178551669 178555670 1.8E+08 178792194 145 15 70715123 70719124 7.1E+07 70784668 146 7 123664155 123668156 1.2E+08 123768284 147 10 31273317 31277318 3.1E+07 31439545 148 10 31271630 31275631 3.2E+07 31524442 149 10 31435544 31439545 3.1E+07 31462965

TABLE 30.F1 150 ZEB1_10_31437913_31439545_31463562_31470397_FR ZEB1 181 122 2.83212E−10 3.70535E−08 151 ZFHX3_16_73147488_73153243_73182254_73184585_FF ZFHX3 200 131 1.15564E−09 1.13397E−07 152 ADRB3_8_37962724_37965269_37987735_37989039_FR ADRB3 29 12 0.689607935 1 153 ADRB3_8_37962724_37965269_38014799_38016599_FR ADRB3 29 12 0.689607935 1 154 AGT_1_230717799_230719628_230752057_230757333_RF AGT 47 33 0.000290665 0.006914309 155 AGT_1_230724515_230729957_230752057_230757333_RF AGT 47 33 0.000290665 0.006914309 156 BMPR1B_4_94967703_94973952_95026184_95035151_FR BMPR1B 200 87 0.614370341 1 157 HTR2A_13_46860092_46866824_46904346_46907815_RF HTR2A 87 42 0.259371991 0.827670783 158 PPARA_22_46101029_46102611_46241078_46244347_FR PPARA 47 28 0.025050129 0.159872776 159 SOS1_2_38982199_38993639_39061418_39066028_FF SOS1 200 83 0.805923582 1 160 SVEP1_9_110493529_110499578_110527410_110532406_FR SVEP1 189 101 0.006989682 0.066107233 161 UBE3A_15_25355032_25368345_25399797_25404434_FF UBE3A 154 109 2.51446E−11  3.9477E−09 162 UBE3A_15_25355032_25368345_25457129_25464700_FR UBE3A 154 109 2.51446E−11  3.9477E−09 163 ACBD6_1_180431719_180434683_180541491_180549122_RR ACBD6 200 111 0.00091339  0.014340227 164 BMPR1B_4_94821712_94826817_94866803_94871889_FF BMPR1B 200 87 0.614370341 1 165 HADHA_2_26188355_26191067_26247231_26249308_FR HADHA 47 27 0.047791071 0.253486424 166 HADHA_2_26188355_26191067_26280650_26284864_FF HADHA 47 27 0.047791071 0.253486424 167 MTFR1_8_65658401_65661888_65780891_65782535_RF MTFR1 184 76 0.812499278 1 168 MYBPC1_12_101567479_101571538_101655128_101656342_RF MYBPC1 186 94 0.05009075  0.263900932 169 MYH1_17_10502067_10505465_10533547_10534931_RF MYH1 103 52 0.121185055 0.485358512 170 MYL1_2_210288997_210291732_210359762_210362293_FF MYL1 10 5 0.476822977 1 171 MYOD1_11_17685862_17689487_17729653_17733608_FR MYOD1 17 6 0.838751191 1 172 NECTIN3_3_111028574_111034204_111209684_111210764_FR NECTIN3 97 52 0.040549948 0.23579044 173 PON1_7_95303795_95305644_95332254_95337348_RF PON1 21 14 0.032634239 0.195038964 174 ACACB_12_109146008_109150083_109236052_109237242_RR ACACB 191 87 0.388279548 1 175 ACACB_12_109236052_109237242_109268078_109273323_RR ACACB 191 87 0.388279548 1 176 COL1A2_7_94359704_94366215_94394399_94397338_RF COL1A2 47 26 0.08460057  0.378025067 177 COX6A1_12_120397017_120399520_120449180_120450939_RF COX6A1 22 5 0.990048121 1 178 GGPS1_1_235284158_235288561_235306299_235310474_FR GGPS1 29 5 0.999501849 1 179 GSN_9_121182946_121189020_121323589_121328431_FF GSN 200 80 0.902128149 1

TABLE 30.F2 150 67.4 0.32502 0.32502 3.52284 0.00229 0.00784 −2.07823 1.25268 1.25268 1 E_Ctrl 151 65.5 −0.43734 −0.43734 −7.5712 4.7E−07 2.3E−05 6.48808 0.7385 −1.3541 −1 Str_Trn 152 41.38 −0.4318 −0.4318 −3.39512 0.00316 0.01261 −2.27663 0.74134 −1.34892 −1 Str_Trn 153 41.38 −0.32388 −0.32388 −4.68737 0.00016 0.00094 0.53671 0.79892 −1.25169 −1 Str_Trn 154 70.21 −0.43415 −0.43415 −3.86294 0.00111 0.00583 −1.25218 0.74013 −1.35111 −1 Str_Trn 155 70.21 −0.463 −0.463 −4.19239 0.00053 0.00337 −0.52301 0.72548 −1.3784 −1 Str_Trn 156 43.5 −0.46141 −0.46141 −4.19386 0.00053 0.00336 −0.51977 0.72628 −1.37689 −1 Str_Trn 157 48.28 −0.45067 −0.45067 −8.32753 1.2E−07 9.1E−06 7.85656 0.73171 −1.36667 −1 Str_Trn 158 59.57 −0.33358 −0.33358 −9.83579 7.2E−09 5.5E−07 10.6041 0.79356 −1.26014 −1 Str_Trn 159 41.5 −0.31318 −0.31318 −6.096 7.5E−06 8.5E−05 3.62327 0.80487 −1.24244 −1 Str_Trn 160 53.44 −0.42515 −0.42515 −9.26758 2.4E−08 2.8E−06 9.44872 0.74476 −1.34271 −1 Str_Trn 161 70.78 −0.20195 −0.20195 −3.01457 0.00716 0.01948 −3.18176 0.86938 −1.15025 −1 Str_Trn 162 70.78 −0.24775 −0.24775 −2.82758 0.01079 0.02719 −3.57372 0.84221 −1.18735 −1 Str_Trn 163 55.5 −0.43863 −0.43863 −7.21561 7.7E−07 1.5E−05 5.91252 0.73784 −1.35531 −1 Str_Trn 164 43.5 −0.40597 −0.40597 −5.58481 2.2E−05 0.00019 2.52537 0.75473 −1.32498 −1 Str_Trn 165 57.45 −0.39201 −0.39201 −14.4017 1.9E−11 2.6E−08 16.364 0.76207 −1.31222 −1 Str_Trn 166 57.45 −0.19239 −0.19239 −1.68433 0.10907 0.18026 −5.55862 0.87515 −1.14266 −1 Str_Trn 167 41.3 −0.37341 −0.37341 −11.7997 3.7E−10 7.6E−08 13.5612 0.77195 −1.29541 −1 Str_Trn 168 50.54 −0.42597 −0.42597 −4.76806 0.00014 0.00081 0.71784 0.74434 −1.34348 −1 Str_Trn 169 50.49 −0.43395 −0.43395 −7.77363 2.7E−07 6.9E−06 6.98965 0.74023 −1.35093 −1 Str_Trn 170 50 −0.38919 −0.38919 −13.7412 2.7E−11 1.4E−08 16.0955 0.76356 −1.30966 −1 Str_Trn 171 35.29 −0.4449 −0.4449 −11.7045 4.2E−10 8.2E−08 13.4275 0.73463 −1.36122 −1 Str_Trn 172 53.61 −0.36776 −0.36776 −7.28424 6.8E−07 1.4E−05 6.04732 0.77498 −1.29035 −1 Str_Trn 173 66.67 −0.39554 −0.39554 −9.56195 1.1E−08 7.4E−07 10.156 0.76021 −1.31543 −1 Str_Trn 174 45.55 0.3764 0.3764 5.78418 1.6E−05 0.00028 2.93947 1.29809 1.29809 1 E_Ctrl 175 45.55 0.36198 0.36198 6.81205   2E−06 6.7E−05 5.03386 1.28519 1.28519 1 E_Ctrl 176 55.32 0.2558 0.2558 5.00789 7.9E−05 0.00053 1.254 1.194 1.194 1 E_Ctrl 177 22.73 0.30181 0.30181 5.45361   3E−05 0.00024 2.23895 1.23269 1.23269 1 E_Ctrl 178 17.24 0.29388 0.29388 2.41607 0.02598 0.05481 −4.39757 1.22593 1.22593 1 E_Ctrl 179 40 0.2534 0.2534 3.85238 0.00108 0.00427 −1.34367 1.19202 1.19202 1 E_Ctrl

TABLE 30.F3 150 GTGTTCTAGATGAGGGGAACAGTGGTGATC 10 31439514 31439545 31463562 31463593 GACTGTGAGGATGAACTAAAAGCAAACCAT 151 CTCTCAACTTTGGATGTAAGAATCATCTTC 16 73153212 73153243 73184554 73184585 GAGATTTTGACTCTCCACCTGCCCCACAGG 152 CGGTCCCTCTGCCCCGGTTACCTACCCGTC 8 37965238 37965269 37987735 37987766 GACATGACACTTGGGTGGGGATACAGGGCC 153 CGGTCCCTCTGCCCCGGTTACCTACCCGTC 8 37965238 37965269 38014799 38014830 GAAGTGGAATGAAGGAGCTTCTAAGTCATA 154 TCCCCCTCTTCCTCTGCCTCCCTTCCCCTC 1 230717799 230717830 230757302 230757333 GATTTGTAAAATGGGCTCATTAGGGAAAAG 155 TCCCCCTCTTCCTCTGCCTCCCTTCCCCTC 1 230724515 230724546 230757302 230757333 GAAAACTGATTAAAAAGAATATTGCTGGCT 156 AATTACTAAGAAAAAAGTGGTTACAATGTC 4 94973921 94973952 95026184 95026215 GAAGAACATAAATATTATGTGGAGACTTAT 157 TCACTTTTATTTATCTTACTCACTTTTCTC 13 46860092 46860123 46907784 46907815 GAGGAATTCTCAGAATTCTCCTCAACCCAC 158 ACACCTCACCCACCCAGCTGGGCTGGCCTC 22 46102580 46102611 46241078 46241109 GATGCCATTAAATCATCCCGTGACCTTCCT 159 TTTCTTCCAACTGAGAGAATCTTAAAAATC 2 38993608 38993639 39065997 39066028 GAAATTGGATAAGGAAAAAAGTGAAATGTG 160 TTATGGCTTAGAAGTAGAAAGTCATAAATC 9 110499547 110499578 110527410 110527441 GATTCCTAAAAATTAATGAGGTGAATAGTA 161 GTTATCAATTTTACTTATAAGACCTATTTC 15 25368314 25368345 25404403 25404434 GAGGTATTAAGGGTTGGAATGAAAAATACA 162 GTTATCAATTTTACTTATAAGACCTATTTC 15 25368314 25368345 25457129 25457160 GATGCAAAAGACAACAAAGTAGGATTTTCA 163 TTTTAGTTTTATTTATTTAGTTATCATCTC 1 180431719 180431750 180541491 180541522 GAAAAACAAACAACAATAACAGCAACCCTC 164 TGAAATCAATAGTTTTATATTAGTCGTATC 4 94826786 94826817 94871858 94871889 GAGCATTCTAGAATCAAACCTTGGGGTATT 165 TACCTTCCAACAGGAAGTGCAAACTAATTC 2 26191036 26191067 26247231 26247262 GATCCTACCCTACCCTACCCTGGAGTTTCC 166 TACCTTCCAACAGGAAGTGCAAACTAATTC 2 26191036 26191067 26284833 26284864 GAATAAGAACCTCGTTATTCATGTTCCTCT 167 TTTCTATGAAGAATGTTCAAGATGCAATTC 8 65658401 65658432 65782504 65782535 GAGCTACATACTATTATATATTTTCACAGT 168 AAATAATAACAAATATGACAGATATTGATC 12 101567479 101567510 101656311 101656342 GATGTCTTAACTTGCCACAGAGATATTTTC 169 GCAAGACTTTGTCTCAAAACAAAAGTGTTC 17 10502067 10502098 10534900 10534931 GAAAAAGTCATCGTTTAAAAGGTAAAATGT 170 AATTTCACATTGATACATTGATAGACATTC 2 210291701 210291732 210362262 210362293 GAAATCATACACAGCATACTCTCAAACCAT 171 TCCATTAGCTCTGCTTTCAAATACTATATC 11 17689456 17689487 17729653 17729684 GATGTAGCTTATGTAAAATAAATGTATTAA 172 TCAAAGTTACAGTTTATATAATTAGAAATC 3 111034173 111034204 111209684 111209715 GATCTAACCTCAATTCCAGTCCCACAAATG 173 TAGAATTATAATACATTCCAAGCTCTTTTC 7 95303795 95303826 95337317 95337348 GAAAAATTCGCATTCCTTGGTCAAGAAAAC 174 TCAAGAAAAAATAATAATAATTTTTTTTTC 12 109146008 109146039 109236052 109236083 GAACTTATGGCTCAAGCGATTCTCTTGCTT 175 AAGCAAGAGAATCGCTTGAGCCATAAGTTC 12 109236052 109236083 109268078 109268109 GATGCTGCTTTGGGAACTGAAGGTTTTTCT 176 AACATACTTTCCTAAATTTTACCTTTTTTC 7 94359704 94359735 94397307 94397338 GAGAAAACATGGACATAAAGATGGCAACAA 177 GGCAGGCAGATCACTTTAGGTCAGGAGTTC 12 120397017 120397048 120450908 120450939 GAACTCCTGACTTCAAGTGATTCGCCCACC 178 ATCTTTCTACATCAGTAAACACAAACTGTC 1 235288530 235288561 235306299 235306330 GAGACCATCCTGGCTAAGACAGTGAAACCC 179 CTCTATAAATTTACCAGAATATAAATTCTC 9 121188989 121189020 121328400 121328431 GACTAAAAGTTCAGTTCTTCATTCCCACTA

TABLE 30.F4 150 10 31435544 31439545 3.1E+07 31467563 151 16 73149242 73153243 7.3E+07 73184585 152 8 37961268 37965269 3.8E+07 37991736 153 8 37961268 37965269 3.8E+07 38018800 154 1 230717799 230721800 2.3E+08 230757333 155 1 230724515 230728516 2.3E+08 230757333 156 4 94969951 94973952 9.5E+07 95030185 157 13 46860092 46864093 4.7E+07 46907815 158 22 46098610 46102611 4.6E+07 46245079 159 2 38989638 38993639 3.9E+07 39066028 160 9 110495577 110499578 1.1E+08 110531411 161 15 25364344 25368345 2.5E+07 25404434 162 15 25364344 25368345 2.5E+07 25461130 163 1 180431719 180435720 1.8E+08 180545492 164 4 94822816 94826817 9.5E+07 94871889 165 2 26187066 26191067 2.6E+07 26251232 166 2 26187066 26191067 2.6E+07 26284864 167 8 65658401 65662402 6.6E+07 65782535 168 12 101567479 101571480  1E+08 101656342 169 17 10502067 10506068 1.1E+07 10534931 170 2 210287731 210291732 2.1E+08 210362293 171 11 17685486 17689487 1.8E+07 17733654 172 3 111030203 111034204 1.1E+08 111213685 173 7 95303795 95307796 9.5E+07 95337348 174 12 109146008 109150009 1.1E+08 109240053 175 12 109236052 109240053 1.1E+08 109272079 176 7 94359704 94363705 9.4E+07 94397338 177 12 120397017 120401018 1.2E+08 120450939 178 1 235284560 235288561 2.4E+08 235310300 179 9 121185019 121189020 1.2E+08 121328431

TABLE 30.G1 180 HTR2A_13_46847106_46857832_46938758_46942222_RF HTR2A 87 42 0.259371991 0.827670783 181 HTR2A_13_46877712_46880636_46938758_46942222_FF HTR2A 87 42 0.259371991 0.827670783 182 IGF1R_15_98652565_98657862_98731539_98737034_RF IGF1R 200 106 0.008018013 0.06952724 183 MUSK_9_110648469_110652659_110747866_110751903_FR MUSK 154 75 0.152643976 0.578867253 184 MYOT_5_137829466_137834410_137882068_137884626_RR MYOT 75 20 0.999459925 1 185 PPARA_22_46128634_46134707_46231440_46235124_FR PPARA 47 28 0.025050129 0.159872776 186 PPP1R9A_7_94903925_94908776_94951930_94967018_RF PPP1R9A 200 113 0.000335824 0.007753573 187 PPP1R9A_7_94951930_94967018_95061734_95065150_FR PPP1R9A 200 113 0.000335824 0.007753573 188 PPP1R9A_7_94951930_94967018_95258927_95267729_FF PPP1R9A 200 113 0.000335824 0.007753573 189 RB1_13_48378062_48381344_48486008_48495146_FF RB1 189 84 0.509778071 1 190 SLC25A13_7_96209525_96214524_96295606_96302029_FF SLC25A13 200 105 0.011714369 0.093834484 191 ACE2_X_15558483_15561359_15624288_15632375_RR ACE2 34 23 0.005085953 0.051850296 192 DNAH5_5_13907228_13913186_13947622_13950495_FR DNAH5 200 106 0.008018013 0.06952724 193 EMCN_4_100636305_100649860_100744427_100745788_RR EMCN 200 121 2.82028E−06 0.000158137 194 ITGAV_2_186622411_186639782_186682119_186696186_RR ITGAV 38 16 0.665375941 1 195 MSTN_2_190044593_190053476_190068550_190073029_FR MSTN 11 5 0.58381774  1 196 PLCXD2_3_111633890_111638317_111672672_111677327_FR PLCXD2 200 76 0.969310539 1 197 SGCZ_8_14631157_14642508_14778176_14785491_FF SGCZ 200 131 1.15564E−09 1.13397E−07 198 SLC25A13_7_96178122_96182739_96295606_96302029_RF SLC25A13 200 105 0.011714369 0.093834484 199 SOCS7_17_38347510_38348776_38360864_38363420_FR SOCS7 47 25 0.139363472 0.533660124 200 SRI_7_88199682_88203042_88229166_88237101_RF SRI 61 34 0.047542529 0.253486424 201 STXBP4_17_55035186_55042800_55117598_55123347_RR STXBP4 178 72 0.865724188 1 202 SVEP1_9_110397951_110405969_110503630_110509758_FF SVEP1 189 101 0.006989682 0.066107233

TABLE 30.G2 180 48.28 0.23347 0.23347 2.92357 0.00875 0.02288 −3.37367 1.17566 1.17566 1 E_Ctrl 181 48.28 0.31362 0.31362 5.2027 5.2E−05 0.00037 1.68658 1.24282 1.24282 1 E_Ctrl 182 53 0.23289 0.23289 2.56313 0.01907 0.04289 −4.11013 1.17519 1.17519 1 E_Ctrl 183 48.7 0.30041 0.30041 3.63015 0.00179 0.00643 −1.84018 1.23149 1.23149 1 E_Ctrl 184 26.67 0.26883 0.26883 6.70047 2.2E−06 3.3E−05 4.88 1.20483 1.20483 1 E_Ctrl 185 59.57 0.29923 0.29923 2.46766 0.02333 0.05033 −4.29772 1.23049 1.23049 1 E_Ctrl 186 56.5 0.29403 0.29403 4.70344 0.00016 0.00091 0.57281 1.22606 1.22606 1 E_Ctrl 187 56.5 0.28471 0.28471 4.35389 0.00035 0.00171 −0.21427 1.21816 1.21816 1 E_Ctrl 188 56.5 0.2709 0.2709 3.54424 0.00218 0.00753 −2.03086 1.20656 1.20656 1 E_Ctrl 189 44.44 0.30464 0.30464 6.97933 1.2E−06 2.2E−05 5.44345 1.23511 1.23511 1 E_Ctrl 190 52.5 0.31224 0.31224 5.62896   2E−05 0.00018 2.62135 1.24163 1.24163 1 E_Ctrl 191 67.65 0.32899 0.32899 9.15537 2.2E−08 1.2E−06 9.47318 1.25614 1.25614 1 E_Ctrl 192 53 0.3725 0.3725 11.9417   3E−10 6.9E−08 13.7588 1.2946 1.2946 1 E_Ctrl 193 60.5 0.31985 0.31985 5.68628 1.8E−05 0.00016 2.74564 1.2482 1.2482 1 E_Ctrl 194 42.11 0.35248 0.35248 2.33791 0.03054 0.06245 −4.54674 1.27675 1.27675 1 E_Ctrl 195 45.45 0.22853 0.22853 2.5176 0.021  0.04632 −4.20002 1.17164 1.17164 1 E_Ctrl 196 38 0.37187 0.37187 9.14346 2.3E−08 1.2E−06 9.45286 1.29403 1.29403 1 E_Ctrl 197 65.5 0.35186 0.35186 12.46 1.5E−10 4.6E−08 14.4629 1.2762 1.2762 1 E_Ctrl 198 52.5 0.3227 0.3227 8.1037 1.4E−07 4.6E−06 7.60648 1.25067 1.25067 1 E_Ctrl 199 53.19 0.32563 0.32563 8.97975   3E−08 1.5E−06 9.17168 1.25321 1.25321 1 E_Ctrl 200 55.74 0.3451 0.3451 6.86348 1.6E−06 2.6E−05 5.21065 1.27024 1.27024 1 E_Ctrl 201 40.45 0.34798 0.34798 7.97475 1.8E−07 5.4E−06 7.36728 1.27277 1.27277 1 E_Ctrl 202 53.44 0.32848 0.32848 4.83516 0.00012 0.00072 0.86819 1.25569 1.25569 1 E_Ctrl

TABLE 30.G3 180 CCAAAAGTAATGGCAACAAAAGTCAAAATC 13 46847106 46847137 46942191 46942222 GATTCTTGGGAATTTCCCAAAATACTGAAA 181 GGCAGGCGGATCTCCTGAGGTCAGGAGATC 13 46880605 46880636 46942191 46942222 GATTTTGACTTTTGTTGCCATTACTTTTGG 182 CGTAGAACTAAGATGTATTCAAAGTCAGTC 15 98652565 98652596 98737003 98737034 GAAAAAGATTAGAAAAGTTCAACTCTAAGA 183 ATCTTACAAAGAATAATTCTAAGAAAAGTC 9 110652628 110652659 110747866 110747897 GAGCATTGGAGAAAATCTCCCTTTTCTTTT 184 CAAAACAATTTGTTAACTTTTTTTTTTTTC 5 137829466 137829497 137882068 137882099 GATTGATGAAGGAAGATTCTGCAGAATGGA 185 TGTTTTTATTTTCATGTTTTAATTTTGTTC 22 46134676 46134707 46231440 46231471 GAACTCTTGACCTCAGGTAAACCACCCACC 186 AGAACTGGTTATTGATCTATTCAGGGATTC 7 94903925 94903956 94966987 94967018 GAAATAATAGATTATGAATAAATTATTCTG 187 AGAACTGGTTATTGATCTATTCAGGGATTC 7 94966987 94967018 95061734 95061765 GAATGAATGAATGAAAATAAAGAGCCATGG 188 AGAACTGGTTATTGATCTATTCAGGGATTC 7 94966987 94967018 95267698 95267729 GAAGGGTAAATACTTAAGTCTTTAAATAAA 189 TTAAAAGCCTTTGATTTTTACAAAGTGATC 13 48381313 48381344 48495115 48495146 GAGTCAGTTTCCTTTTGGTATAAGGATATC 190 GGCAGGCGGATCATTTCAGGTCAGGAGTTC 7 96214493 96214524 96301998 96302029 GACCTGAAATTTCCATACTAAATTTAAATA 191 AAATAAGAAGAAGAAAGGAAAAAAATCTTC X 15558483 15558514 15624288 15624319 GAAAGAGCGTAAGATAGAGAATAATTATTT 192 TTGTTTGTAAATTGTTTTTCTAAAATCTTC 5 13913155 13913186 13947622 13947653 GAGAGCTGGTTGAAAATTTTGCTCTCAATT 193 GGTATTACCTTGATGGCCTTAAAGAAGATC 4 100636305 100636336 100744427 100744458 GAGCCAGAGGGCCTCTGTTCATGTTTGGGC 194 AGAAGACTCACCAAAATTTTATCCTGTTTC 2 186622411 186622442 186682119 186682150 GAACCTTATAATGGTGATAAATCATTAATG 195 TTCCAAATACTTCCTCTGCAAAATGCCATC 2 190053445 190053476 190068550 190068581 GAACTCCTGGCCTCAAGTCATCCATCCGCC 196 CTTTTTGAAGATTATAATCTATTAGTGATC 3 111638286 111638317 111672672 111672703 GAGGCTTTTTTGCTTTTTTTTTTTTGAGAT 197 CTATATGTAAGTTACAATATGTAAGGTATC 8 14642477 14642508 14785460 14785491 GATAGTCACTGAGACTAATTTAATGTTATA 198 TATTTAAATTTAGTATGGAAATTTCAGGTC 7 96178122 96178153 96301998 96302029 GAAGGCACTGAATGTCAGAGCCAAGCTGTA 199 AGGCAGGCAGATCAATGAGGTTGGGAGATC 17 38348745 38348776 38360864 38360895 GACAAGTTCAGTAATTCTGAGGTGAGTTTT 200 TGTAGGCAGATTACCTGAAGTTAGGAGTTC 7 88199682 88199713 88237070 88237101 GATTAGGAATAACCTATCATTAGAGTTGTT 201 GTTGTTATAACTATATCATGAGACTAAGTC 17 55035186 55035217 55117598 55117629 GAAAAAAAAAAACAATAATTTCAGCTGTAT 202 TATATTAGAAACATGTCTGAAAAAAGTATC 9 110405938 110405969 110509727 110509758 GATAAATGTATACGTTGATGTACATTGATA

TABLE 30.G4 180 13 46847106 46851107 4.7E+07 46942222 181 13 46876635 46880636 4.7E+07 46942222 182 15 98652565 98656566 9.9E+07 98737034 183 9 110648658 110652659 1.1E+08 110751867 184 5 137829466 137833467 1.4E+08 137886069 185 22 46130706 46134707 4.6E+07 46235441 186 7 94903925 94907926 9.5E+07 94967018 187 7 94963017 94967018 9.5E+07 95065735 188 7 94963017 94967018 9.5E+07 95267729 189 13 48377343 48381344 4.8E+07 48495146 190 7 96210523 96214524 9.6E+07 96302029 191 X 15558483 15562484 1.6E+07 15628289 192 5 13909185 13913186 1.4E+07 13951623 193 4 100636305 100640306  1E+08 100748428 194 2 186622411 186626412 1.9E+08 186686120 195 2 190049475 190053476 1.9E+08 190072551 196 3 111634316 111638317 1.1E+08 111676673 197 8 14638507 14642508 1.5E+07 14785491 198 7 96178122 96182123 9.6E+07 96302029 199 17 38344775 38348776 3.8E+07 38364865 200 7 88199682 88203683 8.8E+07 88237101 201 17 55035186 55039187 5.5E+07 55121599 202 9 110401968 110405969 1.1E+08 110509758

TABLE 31.a Probe GeneLocus Probe_Count_Total Probe_Count_Sig 1 ClGALT1_7_7113076_7114831_7258228_7260668_FF C1GALT1 89 52 2 DKK3_11_11956071_11968035_11984245_11993733_FR DKK3 54 36 3 FBXO32_8_123526212_123527874_123555254_123559065_FR FBXO32 41 26 4 GPC6_13_94054831_94060621_94121445_94133208_RF GPC6 166 105 5 GSN_9_121177548_121180410_121268506_121274144_FR GSN 156 76 6 LMO4_1_87315524_87318670_87343110_87349940_FF LMO4 105 75 7 MAPK10_4_86572598_86581486_86617317_86621940_FF MAPK10 172 107 8 MBNL1_3_152229500_152234786_152281057_152285843_FR MBNL1 145 85 9 PCK1_20_57527297_57530814_57579772_57583521_RR PCK1 36 26 10 PIK3C3_18_42070009_42072187_42088671_42094691_FF PIK3C3 141 89 11 PTPRC_1_198595771_198598296_198659753_198666156_RF PTPRC 185 91 12 RGS6_14_72139099_72144564_72213251_72222544_FR RGS6 174 104 13 RUNX3_1_24920810_24923822_24973522_24976037_RF RUNX3 51 24 14 ZFHX3_16_73147488_73153243_73182254_73184585_FF ZFHX3 171 123 15 MYOT_5_137829466_137834410_137882068_137884626_RR MYOT 35 20 16 AGT_1_230724515_230729957_230752057_230757333_RF AGT 47 31 17 MYL1_2_210288997_210291732_210359762_210362293_FF MYL1 9 5 18 SRI_7_88199682_88203042_88229166_88237101_RF SRI 57 30

TABLE 31.b HyperG_Stats FDR_HyperG Percent_Sig logFC AveExpr 1 0.485083555 1 58.43 −0.555546218 −0.555546218 2 0.113222201 0.567553327 66.67 −0.452190179 −0.452190179 3 0.279504208 0.898561555 63.41 −0.428908404 −0.428908404 4 0.081947099 0.503453115 63.25 0.528815395 0.528815395 5 0.990051008 1 48.72 −0.435924362 −0.435924362 6 0.002438643 0.079967184 71.43 −0.425303631 −0.425303631 7 0.127316337 0.601206787 62.21 0.369477889 0.369477889 8 0.440065203 1 58.62 −0.423225201 −0.423225201 9 0.052274012 0.438252195 72.22 −0.454377101 −0.454377101 10 0.108139211 0.559937306 63.12 0.349058418 0.349058418 11 0.991656906 1 49.19 0.342871898 0.342871898 12 0.312185766 0.950015156 59.77 0.373553959 0.373553959 13 0.95196413  1 47.06 0.364233402 0.364233402 14 7.53E−05 0.010367006 71.93 −0.437339546 −0.437339546 15 0.594268263 1 57.14 0.377641822 0.377641822 16 0.156967939 0.666487236 65.96 −0.462997504 −0.462997504 17 0.682316487 1 55.56 −0.356584057 −0.356584057 18 0.816232021 1 52.63 0.347423032 0.347423032

TABLE 31.c t P.Value adj.P.Val B 1 −11.0417245 0.00000000111 0.000000163 12.47094565 2 −4.498338722 0.000266954 0.002046882 0.154483715 3 −11.06651685 0.00000000106 0.000000159 12.50758304 4 2.192030297 0.041519144 0.085450094 −4.70897528 5 −4.024149814 0.000771506 0.004457333 −0.895719572 6 −4.334227249 0.000385015 0.002678159 −0.20873374 7 10.62330419 0.00000000289295572819759 0.000000681985048919552 11.54687815 8 −5.762419013 0.0000171628795759885 0.000292745 2.893666517 9 −3.146677782 0.005488024 0.018949968 −2.809655881 10 10.19574365 0.00000000406 0.000000379 11.17917387 11 12.24688433 0.000000000196 0.0000000539 14.17658691 12 9.049855001 0.000000034856893346579 0.0000036264507177386 9.09037332 13 10.30993314 0.00000000464664280056321 0.000000961862645683259 11.08156058 14 −7.571199723 0.000000474476333843650 0.0000231189585700664 6.488080595 15 10.49506981 0.00000000350762736065339 0.000000777454166573518 11.35784279 16 −4.192393926 0.00052891 0.00336987 −0.523006115 17 −7.810248605 0.000000305171587917033 0.0000169792808595093 6.929231219 18 5.646538925 0.0000219157968101507 0.000348185 2.648883369

TABLE 31.d FC FC_1 LS Loop Detected 1 0.680399404 −1.469724979 −1 E_Trn 2 0.730932365 −1.36811564 −1 Str_Trn 3 0.742823621 −1.346214596 −1 E_Trn 4 1.442744064 1.442744064 1 Str_Ctrl 5 0.739219971 −1.352777305 −1 Str_Trn 6 0.744681988 −1.342855092 −1 Str_Trn 7 1.291885213 1.291885213 1 Str_Ctrl 8 0.745755594 −1.34092189 −1 Str_Trn 9 0.729825214 −1.370191083 −1 Str_Trn 10 1.27372905 1.27372905 1 E_Ctrl 11 1.26827878 1.26827878 1 E_Ctrl 12 1.295540359 1.295540359 1 Str_Ctrl 13 1.287197476 1.287197476 1 Str_Ctrl 14 0.738495203 −1.354104937 −1 Str_Trn 15 1.299216466 1.299216466 1 Str_Ctrl 16 0.725477359 −1.378402768 −1 Str_Trn 17 0.781011633 −1.280390659 −1 Str_Trn 18 1.272286016 1.272286016 1 Str_Ctrl

TABLE 31.e Probe sequence Probe Location 60 mer Chr Start1 1 AAATGTATAAGAACAGAAGAGAATTATCTCGACATGTCTGAAAAGTATTATCAGCCCTCT 7 7114800 2 GACACCTCCTCTCCCTTCCCTCCCCTTCTCGAGTTATCAAAATATTTTGAGAGACAGTAT 11 11968004 3 TGCAGAAAGTACTACAAAAAAAGAAGCTTCGAAAATGTTGGAGATGAGAGTTTCTTCACC 8 123527843 4 AATTAGACAACGACTATATGACTCTGTCTCGACTTTAAAGCAAGTACTTCTTGTATGCTC 13 94054831 5 AAAAAGAGAAAAGCAGGTTAGCACATTGTCGACCCCGCCCCCGGGATGGGGGAACTGGCC 9 121180379 6 CCCCTGGCTCACCTACACAAAATTGTGCTCGACTCTACTCTTAGCCCTGCTAAATAAGTA 1 87318639 7 ATTATATTAGTGCTGTAATAAAATTAAGTCGACACATTTGATACTGCTTATTGGGTTATT 4 86581455 8 TACCTTGAAAAGCTCTTCAGTATGATTATCGAGCTTTAGCCATTCTAGTAATTATTAAAA 3 152234755 9 CCTCGTCGTCCCCTCTCTTCCTCGTTCCTCGAACATCTCCAAGTCAGATAATCATAACAA 20 57527297 10 ATCTATTATAATGATGCAATATTGTTAATCGATTCAAAGATCAAATTAATTATTAAAGCT 18 42072156 11 AGAGGCTGAGGTGAAAAGATTGTTTGAGTCGAAGATCATTGTCTCATTTTTTTACTTGTT 1 198595771 12 AATGGCATTCTCCATTTATTCGTATTTATCGAGACTTTCTATGAAAGCTTTTTTGATGTT 14 72144533 13 CTTAATTTTTTTTCTTTGAATGCCTCTATCGACAGTCTTCTCTCTACTTTCTACAGTGAA 1 24920810 14 CTCTCAACTTTGGATGTAAGAATCATCTTCGAGATTTTGACTCTCCACCTGCCCCACAGG 16 73153212 15 CAAAACAATGTGTTAACTTTTTTTTTTTTCGATTGATGAAGGAAGATTCTGCAGAATGGA 5 137829466 16 TCCCCCTCTTCCTCTGCCTCCCTTCCCCTCGAAAACTGATTAAAAAGAATATTGCTGGCT 1 230724515 17 AATTTCACATTGATACATTGATAGACATTCGAAATCATACACAGCATACTCTCAAACCAT 2 210291701 18 TGTAGGCAGATTACCTGAAGTTAGGAGTTCGATTAGGAATAACCTATCATTAGAGTTGTT 7 88199682

TABLE 31.f Probe Location 4 kb Sequence Location End1 Start2 End2 Chr Start1 End1 Start2 End2 1 7114831 7260637 7260668 7 7110830 7114831 7256667 7260668 2 11968035 11984245 11984276 11 11964034 11968035 11984245 11988246 3 123527874 123555254 123555285 8 123523873 123527874 123555254 123559255 4 94054862 94133177 94133208 13 94054831 94058832 94129207 94133208 5 121180410 121268506 121268537 9 121176409 121180410 121268506 121272507 6 87318670 87349909 87349940 1 87314669 87318670 87345939 87349940 7 86581486 86621909 86621940 4 86577485 86581486 86617939 86621940 8 152234786 152281057 152281088 3 152230785 152234786 152281057 152285058 9 57527328 57579772 57579803 20 57527297 57531298 57579772 57583773 10 42072187 42094660 42094691 18 42068186 42072187 42090690 42094691 11 198595802 198666125 198666156 1 198595771 198599772 198662155 198666156 12 72144564 72213251 72213282 14 72140563 72144564 72213251 72217252 13 24920841 24976006 24976037 1 24920810 24924811 24972036 24976037 14 73153243 73184554 73184585 16 73149242 73153243 73180584 73184585 15 137829497 137882068 137882099 5 137829466 137833467 137882068 137886069 16 230724546 230757302 230757333 1 230724515 230728516 230753332 230757333 17 210291732 210362262 210362293 2 210287731 210291732 210358292 210362293 18 88199713 88237070 88237101 7 88199682 88203683 88233100 88237101

TABLE 31.g Inner_primers Probe PCR-Primer1_ID 1 C1GALT1_7_7113076_7114831_7258228_7260668_FF OBD142_025 2 DKK3_11_11956071_11968035_11984245_11993733_FR OBD142_061 3 FBXO32_8_123526212_123527874_123555254_123559065_FR OBD142_089 4 GPC6_13_94054831_94060621_94121445_94133208_RF OBD142_109 5 GSN_9_121177548_121180410_121268506_121274144_FR OBD142_117 6 LMO4_1_87315524_87318670_87343110_87349940_FF OBD142_145 7 MAPK10_4_86572598_86581486_86617317_86621940_FF OBD142_153 8 MBNL1_3_152229500_152234786_152281057_152285843_FR OBD142_157 9 PCK1_20_57527297_57530814_57579772_57583521_RR OBD142_189 10 PIK3C3_18_42070009_42072187_42088671_42094691_FF OBD142_213 11 PTPRC_1_198595771_198598296_198659753_198666156_RF OBD142_233 12 RGS6_14_72139099_72144564_72213251_72222544_FR OBD142_245 13 RUNX3_1_24920810_24923822_24973522_24976037_RF OBD142_253 14 ZFHX3_16_73147488_73153243_73182254_73184585_FF OBD142_325 15 MYOT_5_137829466_137834410_137882068_137884626_RR OBD142_341 16 AGT_1_230724515_230729957_230752057_230757333_RF OBD142_365 17 MYL1_2_210288997_210291732_210359762_210362293_FF OBD142_449 18 SRI_7_88199682_88203042_88229166_88237101_RF OBD142_509

TABLE 31.h Inner_primers Category PCR- High or Low PCR_Primer1 Primer2_ID PCR_Primer2 Responder 1 CACCTCAAAAGACAACCCCAGACCCA OBD142_027 CCCTCACTTTCCTTCTACTCTTCAAG High 2 GCTCCACATTTCCCAATCTAACCTGC OBD142_063 GTCAGAGTTGCCGATAGGTCTTGCTA High 3 AATCTCTGTCCCCAACTGTATCTGGC OBD142_091 ACATCTATCTTGCCCCTCACTCAGGT High 4 GAGTATTTACGATGGTCAGGTGCTGC OBD142_111 ATCCAAACACAGGACGAGAATAAAGC High 5 GACCTGTGGTTCTGACTGTCCAG OBD142_119 TATCGTCCAGGAGGCAAGGGTCC High 6 GCAACCTGGTCTCCTACCTGCTTCTA OBD142_147 GATGAGGTAACCAAAGTTCAGGGAGA High 7 TAGCAGACAATCAGAGGGTTTTGC OBD142_155 CTCTCTCCTCATCCTCCCTCCTAATA High 8 GCTGGTAGTTGGCTTTTGGGAAGAAC OBD142_159 GGGAGCCAGAAAGATAGCAATGCCTA High 9 TTCTCCCTCGGACGCTCATCCTC OBD142_191 GAGGAGGAGAAACTCAGAAGCCC High 10 CTGGAACTTGTTTAGGCACTGAAGCA OBD142_215 GCACAAGACCTCACATTCTGATGGGC High 11 GCAAAGGGCAGGTCATCATCATTCAA OBD142_235 CTCTCCTTTATCCCCTACCCTGCTCA High 12 CCCCGATGAATGTTACCCTGTCCC OBD142_247 CAGAGAAAGGGAGTTTGGAGGGC High 13 CTGAAATCCCATAGTGAGATGCCTTC OBD142_255 CCCCAAACTCCCAGACACATCAGAGA High 14 CCTGGATGTTCATTCCCACCTGG OBD142_327 AGAGGGAAAGGCAGGTCGTGAGC Low 15 GCAGATTCCACAGGGCTTAC OBD142_343 GCTGGTCTCAAACTCCTGGG Low 16 ACCCAACCCTGCTATACAATTCCA OBD142_367 GGGCATCMCCTCTTATTCAAGGT Low 17 ACAGTCAGTGATFGGCACAGAGTAA OBD142_451 AGGAAATAGCCCAAATGCAACTGAA High 18 GAATGAAACTCTGAGGCCGG OBD142_511 CCCATTCGTCTCTCTGAGCTG High

TABLE 31.i Gene Marker GLMNET 1 C1GALT1 OBD142_025.027 0.242638274 2 DKK3 OBD142_061.063 0.147262728 3 FBXO32 OBD142_089.091 −0.087251896 4 GPC6 OBD142_109.111 0.233745002 5 GSN OBD142_117.119 0.294663423 6 LMO4 OBD142_145.147 −0.118956396 7 MAPK10 OBD142_153.155 −0.17796692 8 MBNL1 OBD142_157.159 −0.161065194 9 PCK1 OBD142_189.191 0.196530289 10 PIK3C3 OBD142_213.215 −0.083748281 11 PTPRC OBD142_233.235 0.30236596 12 RGS6 OBD142_245.247 0.078658478 13 RUNX3 OBD142_253.255 0.06399744 14 ZFHX3 OBD142_325.327 0.115886108 15 MYOT OBD142_341.343 −0.049119122 16 AGT OBD142_365.367 0.199239865 17 MYL1 OBD142_449.451 −0.16982619 18 SRI OBD142_509.511 0.129049402

TABLE 32.a Probe GeneLocus Probe_Count_Total Probe_Count_Sig 1 THNSL2_2_88139809_88146295_88161717_88164554_FR THNSL2 29 20 2 IGF1R_15_98652565_98657862_98731539_98737034_RF IGF1R 177 96 3 DKK3_11_11956071_11968035_11984245_11993733_FR DKK3 54 36 4 CBL_11_119249760_119252653_119294588_119299643_RF CBL 24 19 5 EYA1_8_71216399_71218728_71261816_71267769_RR EYA1 139 80 6 ACACB_12_109236052_109237242_109268078_109273323_RR ACACB 133 81 7 PTPRC_1_198595771_198598296_198659753_198666156_RF PTPRC 185 91

TABLE 32.b HyperG_Stats FDR_HyperG Percent_Sig logFC AveExpr t 1 0.147351557 0.651492557 68.97 0.348303621 0.348303621 5.482854907 2 0.840040511 1 54.24 0.376793177 0.376793177 3.580450098 3 0.113222201 0.567553327 66.67 −0.452190179 −0.452190179 −4.498338722 4 0.023815147 0.261918121 79.17 −0.426375519 −0.426375519 −4.618561579 5 0.544172978 1 57.55 −0.420279402 −0.420279402 −6.888734462 6 0.250820309 0.854526334 60.9 0.361980641 0.361980641 6.812052569 7 0.991656906 1 49.19 0.342871898 0.342871898 12.24688433

TABLE 32.c P.Value adj.P.Val B FC FC_1 1 0.0000279 0.000231594 2.302943346 1.273062829 1.273062829 2 0.002089314 0.00927894 −1.873258731 1.298452444 1.298452444 3 0.000266954 0.002046882 0.154483715 0.730932365 −1.36811564 4 0.000204351 0.001696324 0.420007759 0.744128913 −1.343853172 5 0.00000174500366992146 0.0000602085318700566 5.184417423 0.747279887 −1.338186692 6 0.00000202795176244020 0.0000670770127555545 5.033860861 1.285189092 1.285189092 7 0.000000000196 0.0000000539 14.17658691 1.26827878 1.26827878

TABLE 32.d Loop Probe sequence LS Detected 60 mer 1 1 E_Ctrl TATCAAGTTAAACATTCAGACGTCTAGGTCGACTTGAAGTTCACCTAAAGTTTTCCAGTC 2 1 E_Ctrl CGTAGAACTAAGATGTATTCAAAGTCAGTCGAAAAAGATTAGAAAAGTTCAACTCTAAGA 3 −1 Str_Trn GACACCTCCTCTCCCTTCCCTCCCCTTCTCGAGTTATCAAAATATTTTGAGAGACAGTAT 4 −1 Str_Trn ACCGCCTCACCTCAGCTCTCCAGTGAGATCGATCCTCCCACCTAAGCTTCCCAAGTTGCT 5 −1 Str_Trn TGTCCTTTCAAGGAAGGATTAGCATCCTTCGAAAGACCTATCAGGATTTCATTTGTAATG 6 1 E_Ctrl AAGCAAGAGAATCGCTTGAGCCATAAGTTCGATGCTGCTTTGGGAACTGAAGGTTTTTCT 7 1 E_Ctrl AGAGGCTGAGGTGAAAAGATTGTTTGAGTCGAAGATCATTGTCTCATTTTTTTACTTGTT

TABLE 32.e Probe Location Chr Start1 End1 Start2 End2 1 2 88146264 88146295 88161717 88161748 2 15 98652565 98652596 98737003 98737034 3 11 11968004 11968035 11984245 11984276 4 11 119249760 119249791 119299612 119299643 5 8 71216399 71216430 71261816 71261847 6 12 109236052 109236083 109268078 109268109 7 1 198595771 198595802 198666125 198666156

TABLE 32.f 4 kb Sequence Location Chr Start1 End1 Start2 End2 1 2 88142294 88146295 88161717 88165718 2 15 98652565 98656566 98733033 98737034 3 11 11964034 11968035 11984245 11988246 4 11 119249760 119253761 119295642 119299643 5 8 71216399 71220400 71261816 71265817 6 12 109236052 109240053 109268078 109272079 7 1 198595771 198599772 198662155 198666156

TABLE 32.g Inner_primers Probe PCR-Primer1_ID 1 THNSL2_2_88139809_88146295_88161717_88164554_FR OBD142_297 2 IGF1R_15_98652565_98657862_98731539_98737034_RF OBD142_329 3 DKK3_11_11956071_11968035_11984245_11993733_FR OBD142_061 4 CBL_11_119249760_119252653_119294588_119299643_RF OBD142_029 5 EYA1_8_71216399_71218728_71261816_71267769_RR OBD142_081 6 ACACB_12_109236052_109237242_109268078_109273323_RR OBD142_469 7 PTPRC_1_198595771_198598296_198659753_198666156_RF OBD142_233

TABLE 32.h Inner_primers Category PCR- High or Low PCR_Primer1 Primer2_ID PCR_Primer2 Responder 1 GTAACACAGGTAGGAAGGAGTGGAGC OBD142_299 CACCATAAAATAGGGCAAGGTCAGCA High 2 TACTCCTCGTTCCCTTTTCTCTC OBD142_331 TGTGTGCTAGGCTGATATGGTTTG High 3 GCTCCACATTTCCCAATCTAACCTGC OBD142_063 GTCAGAGTTGCCGATAGGTCTTGCTA High 4 ACTGAAGGTTCCCAAGTTCCCGAGAG OBD142_031 TTAGTCTGTATGGTAGTGTGTGCCTG High 5 GGCAAGTTTCCTGACCTCTCTGACAT OBD142_083 GAAGGAGGGAGGTAGGAGAGTCATTA High 6 AGGAATGGTTACTGCTCCTCTTTGT OBD142_471 ATTGAATTCTCTCTGTGGCCTTTGC High 7 GCAAAGGGCAGGTCATCATCATTCAA OBD142_235 CTCTCCTTTATCCCCTACCCTGCTCA High

TABLE 32.i Gene Marker GLMNET 1 THNSL2 OBD142_297.299 0.379691192 2 IGF1R OBD142_329.331 0.248382918 3 DKK3 OBD142_061.063 −0.259421345 4 CBL OBD142_029.031 0.125293919 5 EYA1 OBD142_081.083 −0.165674931 6 ACACB OBD142_469.471 −0.229960031 7 PTPRC OBD142_233.235 −0.066564639

TABLE 33.a1 N Probe GeneLocus Probe_Count_Total Probe_Count_Sig 1 ABCC9_6_47915416_47925286_48134697_48137569_RF ABCC9 1 53 2 ACACA_11_36333514_36339214_36350786_36357493_RR ACACA 4 219 3 ACACA_11_36333514_36339214_36436048_36448276_RR ACACA 4 219 4 ACACA_11_36333514_36339214_36541652_36552356_RF ACACA 4 219 5 ACACA_11_36436048_36448276_36626441_36631346_FF ACACA 4 219 6 ACACB_8_11863063_11867350_11908667_11911946_RR ACACB 1 31 7 ACBD6_5_17677182_17680294_17812085_17822701_FR ACBD6 3 206 8 ACBD6_5_17677182_17680294_17952666_17962707_FF ACBD6 3 206 9 ACBD6_5_17677182_17680294_17952666_17962707_FR ACBD6 3 206 10 AHCYL2_4_84035626_84046686_84262207_84266431_FR AHCYL2 2 209 11 AHCYL2_4_84081753_84093856_84262207_84266431_FR AHCYL2 2 209 12 ANGPTL1_5_13716369_13718618_13770118_13781369_FR ANGPTL1 2 41 13 ANGPTL1_5_13716369_13718618_13770118_13781369_RR ANGPTL1 2 41 14 APC_14_59179179_59182887_59237657_59248555_FF APC 2 76 15 APC_14_59179179_59182887_59237657_59248555_FR APC 2 76 16 APOA2_5_35820030_35830912_35848600_35852478_RF APOA2 3 65 17 APOA2_5_35820030_35830912_35866091_35873759_RR APOA2 3 65 18 APOA2_5_35848600_35852478_35900637_35912475_FR APOA2 3 65 19 BECN1_11_20175502_20184049_20243179_20248279_RF BECN1 3 28 20 BECN1_11_20175502_20184049_20320840_20322495_RF BECN1 3 28 21 BECN1_11_20243179_20248279_20281555_20289129_FR BECN1 3 28 22 BTN1A1_20_24591764_24605263_24706408_24710466_FR BTN1A1 1 122 23 BTNL2_20_32536895_32543196_32585002_32592656_RF BTNL2 6 66 24 BTNL2_20_32570542_32582104_32597196_32598340_RF BTNL2 6 66 25 BTNL2_20_32570542_32582104_32598340_32606017_RR BTNL2 6 66 26 BTNL2_20_32570542_32582104_32672903_32675921_RF BTNL2 6 66 27 BTNL2_20_32585002_32592656_32716550_32722709_FF BTNL2 6 66 28 BTNL2_20_32598340_32606017_32645786_32652591_RR BTNL2 6 66 29 CACNA1G_11_26122948_26135515_26185131_26187822_RF CACNA1G 2 33 30 CACNA1G_11_26122948_26135515_26187822_26192201_RF CACNA1G 2 33 31 CACNA2D3_16_33352821_33354631_33641948_33654248_RF CACNA2D3 14 766 32 CACNA2D3_16_33410233_33413906_33641948_33654248_RF CACNA2D3 14 766 33 CACNA2D3_16_33479236_33480664_33641948_33654248_RF CACNA2D3 14 766 34 CACNA2D3_16_33563090_33565331_33641948_33654248_RF CACNA2D3 14 766 35 CACNA2D3_16_33622760_33627636_33641948_33654248_RF CACNA2D3 14 766 36 CACNA2D3_16_33641948_33654248_33704852_33706847_FF CACNA2D3 14 766 37 CACNA2D3_16_33641948_33654248_33729470_33733482_FF CACNA2D3 14 766 38 CACNA2D3_16_33641948_33654248_33733482_33741095_FF CACNA2D3 14 766 39 CACNA2D3_16_33641948_33654248_33733482_33741095_FR CACNA2D3 14 766 40 CACNA2D3_16_33641948_33654248_33757281_33760491_FF CACNA2D3 14 766 41 CACNA2D3_16_33641948_33654248_33760582_33768051_FR CACNA2D3 14 766 42 CACNA2D3_16_33641948_33654248_33768286_33770169_FR CACNA2D3 14 766 43 CACNA2D3_16_33641948_33654248_33815034_33817501_FR CACNA2D3 14 766 44 CACNA2D3_16_33641948_33654248_33848517_33852225_FF CACNA2D3 14 766 45 CACNB2_29_17033576_17046068_17154781_17155878_RF CACNB2 6 225 46 CACNB2_29_17048693_17053442_17144042_17154089_RR CACNB2 6 225 47 CACNB2_29_17144042_17154089_17262741_17269092_RR CACNB2 6 225 48 CACNB2_29_17144042_17154089_17332733_17336468_RF CACNB2 6 225 49 CACNB2_29_17144042_17154089_17332733_17336468_RR CACNB2 6 225 50 CACNB2_29_17286082_17289972_17348926_17357613_RF CACNB2 6 225 51 CAMK2G_1_61385709_61392305_61537867_61544849_FF CAMK2G 4 87 52 CAMK2G_1_61385709_61392305_61570715_61577474_FF CAMK2G 4 87 53 CAMK2G_1_61385709_61392305_61570715_61577474_FR CAMK2G 4 87 54 CAMK2G_1_61385709_61392305_61578119_61589600_FR CAMK2G 4 87 55 CARD11_13_4269642_4272623_4440946_4446573_RR CARD11 1 31 56 CASP3_27_25376884_25380938_25471835_25478467_RR CASP3 1 60 57 CCNDBP1_1_145659771_145664399_145699582_145711153_RR CCNDBP1 4 96 58 CCNDBP1_1_145659771_145664399_145762480_145771097_RR CCNDBP1 4 96 59 CCNDBP1_1_145659771_145664399_145793388_145800297_RF CCNDBP1 4 96 60 CCNDBP1_1_145659771_145664399_145793388_145800297_RR CCNDBP1 4 96 61 CD19_13_19942675_19947695_20028912_20034792_RF CD19 3 29 62 CD19_13_20002320_20006400_20028912_20034792_RF CD19 3 29 63 CD19_13_20007058_20010478_20028912_20034792_RF CD19 3 29 64 CD2_5_52197323_52200100_52321910_52330791_FF CD2 1 30

TABLE 33.a2 N HyperG_Stats FDR_HyperG Percent_Sig logFC AveExpr 1 0.283590396 0.318114445 1.89 0.320518457 9.948416738 2 0.071740684 0.151713905 1.83 −0.293607855 7.847234944 3 0.071740684 0.151713905 1.83 −0.210300022 8.374350236 4 0.071740684 0.151713905 1.83 0.231385222 8.833918508 5 0.071740684 0.151713905 1.83 −0.305200929 6.737863734 6 0.198752749 0.267074007 3.23 −0.96134378 7.26378007 7 0.149176662 0.267074007 1.46 −0.26093573 9.509514883 8 0.149176662 0.267074007 1.46 −0.258481627 9.295947643 9 0.149176662 0.267074007 1.46 −0.281768793 9.595365742 10 0.266652717 0.310300562 0.96 −0.295771266 9.712393304 11 0.266652717 0.310300562 0.96 −0.335883754 9.167228863 12 0.039967104 0.109696945 4.88 0.305246417 7.108599809 13 0.039967104 0.109696945 4.88 0.30390975 9.437958235 14 0.104263108 0.213491126 2.63 −0.21158792 10.04027255 15 0.104263108 0.213491126 2.63 −0.18597646 10.12135456 16 0.014396814 0.064041001 4.62 −0.285169774 10.6370881 17 0.014396814 0.064041001 4.62 −0.188307832 9.94119358 18 0.014396814 0.064041001 4.62 −0.35682778 10.37459386 19 0.001460812 0.014841655 10.71 −0.806200399 8.954094586 20 0.001460812 0.014841655 10.71 −0.172300256 11.08935116 21 0.001460812 0.014841655 10.71 −0.689404695 9.24381568 22 0.369972517 0.369972517 0.82 −0.188359359 10.5379586 23 0.0000162598909570469 0.000524381 9.09 −0.626172706 7.90082566 24 0.0000162598909570469 0.000524381 9.09 −0.914586684 9.145982862 25 0.0000162598909570469 0.000524381 9.09 −0.419132349 9.090576394 26 0.0000162598909570469 0.000524381 9.09 −0.87421888 9.197203863 27 0.0000162598909570469 0.000524381 9.09 −0.774602225 7.429403071 28 0.0000162598909570469 0.000524381 9.09 −0.630265492 10.1595488 29 0.027478161 0.080560972 6.06 −0.802327215 9.327353317 30 0.027478161 0.080560972 6.06 −0.583404038 9.095292225 31 0.002885548 0.019591352 1.83 0.209398931 11.18280673 32 0.002885548 0.019591352 1.83 0.194627322 11.7177864 33 0.002885548 0.019591352 1.83 0.198440578 11.24724562 34 0.002885548 0.019591352 1.83 0.200166764 10.76693749 35 0.002885548 0.019591352 1.83 0.242678129 10.92474812 36 0.002885548 0.019591352 1.83 0.19266085 11.39119603 37 0.002885548 0.019591352 1.83 0.199552427 11.12621619 38 0.002885548 0.019591352 1.83 0.221089342 11.19545935 39 0.002885548 0.019591352 1.83 0.276958928 10.73545888 40 0.002885548 0.019591352 1.83 0.203939961 11.05986864 41 0.002885548 0.019591352 1.83 0.210750359 11.34843609 42 0.002885548 0.019591352 1.83 0.20067327 11.31423277 43 0.002885548 0.019591352 1.83 0.245046459 10.85328784 44 0.002885548 0.019591352 1.83 0.219462879 10.72704267 45 0.008301566 0.042836079 2.67 −0.593545035 8.631773695 46 0.008301566 0.042836079 2.67 −0.195749334 7.90944735 47 0.008301566 0.042836079 2.67 −0.287774413 9.577708179 48 0.008301566 0.042836079 2.67 −0.274080009 7.326771399 49 0.008301566 0.042836079 2.67 −0.292274875 9.957522807 50 0.008301566 0.042836079 2.67 0.283385806 7.748329166 51 0.005032361 0.029507937 4.6 −0.236733028 11.38171809 52 0.005032361 0.029507937 4.6 −0.484010849 10.01269368 53 0.005032361 0.029507937 4.6 −0.303821538 10.44275862 54 0.005032361 0.029507937 4.6 −0.378665253 10.33209023 55 0.198752749 0.267074007 3.23 −0.205289586 10.29956667 56 0.303088108 0.331342084 1.67 −0.355934967 8.751256232 57 0.006979045 0.037512367 4.17 −0.63182397 10.94820024 58 0.006979045 0.037512367 4.17 −0.696810436 10.48066661 59 0.006979045 0.037512367 4.17 −0.322489712 9.760585457 60 0.006979045 0.037512367 4.17 −0.625156464 10.77930783 61 0.001616117 0.014841655 10.34 −0.390037974 8.434827236 62 0.001616117 0.014841655 10.34 −0.673915806 8.40536563 63 0.001616117 0.014841655 10.34 −0.395313235 7.939097247 64 0.193928419 0.267074007 3.33 −0.259547189 9.581323717

TABLE 33.a3 N t P.Value adj.P.Val B FC 1 7.263712103 0.000000658532712373121 0.000395221 6.182644836 1.248779238 2 −5.291321916 0.0000408766051478055 0.006156743 2.287156198 0.815859225 3 −5.050567397 0.0000698310885505510 0.008902323 1.777241611 0.864357461 4 5.096854125 0.0000629720358323017 0.008441715 1.875717506 1.173961602 5 −5.402991698 0.0000319491285625712 0.005171517 2.521615893 0.809329491 6 −7.453856126 0.000000454451923050407 0.000311021 6.527700337 0.513578324 7 −5.529047183 0.0000242301608260188 0.004416684 2.784577889 0.834546458 8 −5.399685477 0.0000321824586248703 0.005178058 2.514694153 0.835967276 9 −6.654810658 0.00000223206986757685 0.000837241 5.040151004 0.822581886 10 −6.241524808 0.00000525766136243176 0.001576825 4.232788024 0.814636711 11 −6.320309917 0.00000445769617599177 0.001402377 4.388632115 0.792298649 12 5.609172308 0.0000203429879959953 0.0039679 2.950743157 1.235629669 13 7.008043044 0.00000109276077875550 0.000532857 5.709861189 1.23448538 14 −5.526775502 0.0000243508405008230 0.004416684 2.779855512 0.863586191 15 −5.184267596 0.0000518309913407067 0.007221168 2.06113207 0.879053904 16 −5.131092219 0.0000583432064738677 0.007902668 1.948429433 0.820645031 17 −5.090952536 0.0000638069334895659 0.008495251 1.863172915 0.877634514 18 −5.320752831 0.0000383014725598130 0.005929129 2.34908169 0.780879703 19 −10.73162962 0.00000000156642896568417 0.00000555512672284904 11.63110669 0.571886043 20 −5.071479915 0.0000666425700694542 0.008670693 1.821758099 0.887426625 21 −11.43551668 0.000000000543755314186107 0.00000265148685080001 12.53781121 0.620109675 22 −5.281294908 0.0000417937674137867 0.006270673 2.266037132 0.877603169 23 −6.43285853 0.00000352629587947274 0.001196181 4.609695945 0.647892918 24 −5.936360791 0.0000100392087096020 0.002463079 3.620834864 0.53049583 25 −6.27688641 0.00000488175309950516 0.001499505 4.302847451 0.747874268 26 −5.895655257 0.0000109534936492495 0.002605462 3.538234643 0.545549164 27 −5.294894055 0.0000405548509879891 0.006131956 2.294677302 0.584549772 28 −5.091526221 0.0000637252817777454 0.008495251 1.864392502 0.646057513 29 −10.17863513 0.00000000372947965181301 0.00000909293757607660 10.87544294 0.57342344 30 −6.90646185 0.00000133961123275428 0.000598065 5.519220905 0.667387219 31 5.662783116 0.0000181042793666228 0.003741337 3.061481776 1.156206374 32 5.631236286 0.0000193891442127443 0.003919018 2.996361868 1.144428493 33 5.666098866 0.0000179743992793013 0.003741337 3.068319007 1.147457388 34 5.427843178 0.0000302497258239690 0.005000177 2.573603928 1.148831143 35 5.312745619 0.0000389852287177481 0.005987456 2.332243017 1.183187018 36 5.053579322 0.0000693624553048217 0.008871572 1.783655581 1.142869637 37 5.139332812 0.0000572818435901524 0.007813163 1.965913201 1.148342045 38 5.771451184 0.0000143085584536262 0.003153542 3.284832702 1.165613379 39 7.603984521 0.000000340247830958195 0.000270685 6.796180224 1.211638166 40 5.197633668 0.0000503139299503325 0.007169673 2.08941646 1.151839706 41 5.184590564 0.0000517937896507643 0.007221168 2.061815727 1.157289945 42 5.508845037 0.0000253252202636046 0.00443021 2.742560003 1.149234549 43 6.888512233 0.00000138890201289527 0.000606823 5.485369802 1.185130935 44 5.190118523 0.0000511612462532849 0.007206844 2.073515633 1.164300032 45 −5.951345629 0.00000972270336819660 0.002446985 3.651185844 0.662712467 46 −5.006721458 0.0000770300340578710 0.009606804 1.683777572 0.873119281 47 −5.945124115 0.00000985284933645142 0.002463079 3.638588206 0.819164776 48 −5.085844945 0.0000645386031849005 0.00853441 1.852313415 0.826977505 49 −6.066098719 0.00000761463569393438 0.0020486 3.882591854 0.816613388 50 5.41620177 0.0000310339784093617 0.00506542 2.549259461 1.217047779 51 −6.036325672 0.00000811181608888997 0.002138121 3.822727459 0.848664933 52 −8.409111112 0.0000000758476579555309 0.000084511023122425 8.176782156 0.714987116 53 −6.341938105 0.00000426082327745524 0.001351339 4.431257193 0.810103678 54 −7.527123857 0.000000394440182526223 0.000284947 6.659163938 0.76914886 55 −6.66299269 0.00000219503072654509 0.000837079 5.055878269 0.867364567 56 −5.372396859 0.0000341760619744322 0.005375839 2.457516974 0.781363101 57 −12.0166013 0.000000000235462982188889 0.00000183708218703771 13.24249697 0.645359984 58 −12.8061782 0.0000000000793212810435301 0.000000960392461716811 14.14079379 0.616934642 59 −7.657502685 0.000000307118694602961 0.000254909 6.891044499 0.799688634 60 −12.70330829 0.0000000000911214846380425 0.000000960392461716811 14.02745955 0.648349459 61 −5.835579933 0.0000124617597410427 0.002859607 3.415923184 0.763109518 62 −9.840705036 0.00000000644260267107065 0.000013962551677693 10.39393487 0.626803089 63 −5.795472953 0.0000135859288607979 0.00308132 3.334000537 0.760324279 64 −5.940740709 0.00000994561781482989 0.002463079 3.629709305 0.835350065

TABLE 33.a4 Loop Probe sequence N FC_1 LS Detected 60 mer 1 1.248779238 1 Sprinter AAAAAGAAAGAGGGAAGAAGGAAAGAAGTCGATGAAACATGCAGTCAACTTGGGAGGCCC 2 −1.225701652 −1 Stayer ATGAAGGTAATAGTACCTTACCTCGTAGTCGAAAAAAAAATTCCTCCCCATAAAGAGACC 3 −1.156928753 −1 Stayer ATGAAGGTAATAGTACCTTACCTCGTAGTCGATTATCAGCCTTTTTCTTGAAGAACCTCC 4 1.173961602 1 Sprinter AACACAGATGATCATCATAAGACGTAGGTCGACTACGAGGTAAGGTACTATTACCTTCAT 5 −1.23559071 −1 Stayer GATGCAAGTACTTCCTAATTTCTCTAAGTCGAATCAAACTTTAATTTTTAGAAATTCAAA 6 −1.947122673 −1 Stayer ATTTTCATAGCTATTGCATTTAACTCTTTCGAAATTGATTTTTTTTAAATAGATAAGCAA 7 −1.198255639 −1 Stayer ACCAGCAATATTTGTGAGAGTACCAGTTTCGAACTTGATTCACACTGTACTGTGAGCCAG 8 −1.196219074 −1 Stayer ACCAGCAATATTTGTGAGAGTACCAGTTTCGATTTTCTAGAGATGTCCAAGTGTACACTT 9 −1.215684441 −1 Stayer ACCAGCAATATTTGTGAGAGTACCAGTTTCGAGAGAGCTATTGTTTGATGCTGTGTATTC 10 −1.227541046 −1 Stayer TTGCAGTTTGAAGAGATCAGCATTGAAATCGACCCAGCTCAGAAGTACTTCCTGCTGCCC 11 −1.262150329 −1 Stayer TGGTATACTAATTTTACAGATAAAGAAATCGACCCAGCTCAGAAGTACTTCCTGCTGCCC 12 1.235629669 1 Sprinter CCCCAAAATCTTTTATTTCTGTAGAAAATCGACAAATGTAGGTAATAAAAAAACATATGA 13 1.23448538 1 Sprinter TGCAAGTAGAGGATTAGTAGCAGTTAAATCGACAAATGTAGGTAATAAAAAAACATATGA 14 −1.157962008 −1 Stayer ACAGCTCTAGGTTTCTTCAATACGTTTGTCGAAGGCATTCTTTGCAAAGACATTTTTATG 15 −1.137586666 −1 Stayer ACAGCTCTAGGTTTCTTCAATACGTTTGTCGAACCCTAGAAATTAAGCAAATTATAGATA 16 −1.218553653 −1 Stayer TGATGTTGGTATAGAGAGGGCCCAGCTCTCGACTTCAAGACCCACCGAAAGACTGGGACT 17 −1.139426474 −1 Stayer AGTCCCAGTCTTTCGGTGGGTCTTGAAGTCGACTACCACTAAGCTCTCACTACTAAGCTG 18 −1.280606982 −1 Stayer TGATGTTGGTATAGAGAGGGCCCAGCTCTCGAGGGGAATGAAAAATTAAAGGAACTGACC 19 −1.748600115 −1 Stayer ATCTGGTCTATGTCCAGGTACTCTCGGATCGAGGTTAAGAGCATAGACTTTGGAGTTTCA 20 −1.126853727 −1 Stayer TGAGATCAGAGAACAAATTGTCCGGGAGTCGAGGTTAAGAGCATAGACTTTGGAGTTTCA 21 −1.61261796 −1 Stayer ATCTGGTCTATGTCCAGGTACTCTCGGATCGAGTGCAGGTATGTGGAAACATGTTTAGTG 22 −1.139467171 −1 Stayer ACCTGAAGTCAGAGTATGTGTGACAGTTTCGACCACGGGAGGAAAAAAGCGGTCCAAGTA 23 −1.543464933 −1 Stayer TAGAATATGTAGAGATGTCTCCTTTCTATCGATGTGAGTATCAAGCAGTAACCTGAAAAA 24 −1.885028954 −1 Stayer TAGGCAGATAAGGACATATCTGTAATTCTCGAAACAACACCTGTTTATTTGTTTACAGTT 25 −1.337123154 −1 Stayer AACTGTAAACAAATAAACAGGTGTTGTTTCGACAGAAGCAGCACTATGATCTCTCACTGA 26 −1.833015367 −1 Stayer GGTATCAATTATAGCCGTCTACCTTGTGTCGAAACAACACCTGTTTATTTGTTTACAGTT 27 −1.710718313 −1 Stayer TAGAATATGTAGAGATGTCTCCTTTCTATCGACAACACTAGGTTATGGTGTGATAAGGAC 28 −1.547849811 −1 Stayer TCAGTGAGAGATCATAGTGCTGCTTCTGTCGAGTCAGACTATAGCGCTACAGGCAACATG 29 −1.743911968 −1 Stayer ATCCAGACACTCAAGGACTTCCAGTACATCGAATGGCCAAATAATATCCCATTGTATGAA 30 −1.498380509 −1 Stayer TCCTCCTTCACTAGCTCTTGGTGGTACCTCGAATGGCCAAATAATATCCCATTGTATGAA 31 1.156206374 1 Sprinter TCCCTCACACACAAGTCATGCAGTTTTTTCGATTCAGCCAGGCTTAGCTTTTCCAGGGAA 32 1.144428493 1 Sprinter TCCCTCACACACAAGTCATGCAGTTTTTTCGAAGTCAGGGCTCAATGGGCCTTGGGGGGG 33 1.147457388 1 Sprinter TCCCTCACACACAAGTCATGCAGTTTTTTCGAAATTGTCGTTTAATTGCCTAACCTGCAC 34 1.148831143 1 Sprinter TCCCTCACACACAAGTCATGCAGTTTTTTCGACTTGGGTCTTAATTAGGATCTTTTATGC 35 1.183187018 1 Sprinter TCCCTCACACACAAGTCATGCAGTTTTTTCGAATCTCTAAGACTAAAATGAAATCCTGGA 36 1.142869637 1 Sprinter TCCCTCACACACAAGTCATGCAGTTTTTTCGATTTATTTACGTTGGTGGCCACTTGGACT 37 1.148342045 1 Sprinter TCCCTCACACACAAGTCATGCAGTTTTTTCGACCCCAACAAAAATGGAATAAAACCCACC 38 1.165613379 1 Sprinter TCCCTCACACACAAGTCATGCAGTTTTTTCGAAGCTTGTTAAGATCCAGTTTCTGGCCTC 39 1.211638166 1 Sprinter TCCCTCACACACAAGTCATGCAGTTTTTTCGAGTAAACTACATTTTACAGTGTGAAAAAT 40 1.151839706 1 Sprinter TCCCTCACACACAAGTCATGCAGTTTTTTCGAATGTCCCTTACTATTTATTCCCCCAAAT 41 1.157289945 1 Sprinter TCCCTCACACACAAGTCATGCAGTTTTTTCGAATCTGACTCCATCACTTGATCTTGGGCA 42 1.149234549 1 Sprinter TCCCTCACACACAAGTCATGCAGTTTTTTCGACAAACGTCACCTCTGATGGAGAATGCTG 43 1.185130935 1 Sprinter TCCCTCACACACAAGTCATGCAGTTTTTTCGATTGAAGAGTTAATGAAATAACCATAATT 44 1.164300032 1 Sprinter TCCCTCACACACAAGTCATGCAGTTTTTTCGAAAAGGCTGCATACTATATGATTCCGATT 45 −1.508950035 −1 Stayer TGCTATAGAGGCAGCTGTAAATATAAATTCGAAAGTGTAGATTCAGAGATATCACATGGT 46 −1.145318884 −1 Stayer GAAGGCAACCAGCTTGCCTTCTGAAGGATCGAGGGTACATAAGAGGAGTCTACACTATGA 47 −1.220755615 −1 Stayer TCATAGTGTAGACTCCTCTTATGTACCCTCGATGAGGTGGGTAGAATCTTCATTTTAATC 48 −1.209222735 −1 Stayer TTTTTTAAAATTAAAATCATTTTTTGACTCGAGGGTACATAAGAGGAGTCTACACTATGA 49 −1.224569686 −1 Stayer TCATAGTGTAGACTCCTCTTATGTACCCTCGACCTAGAGCTGTTCTCTGGATTCTCAGAA 50 1.217047779 1 Sprinter TAAGGAAATGTAAATGTAAAAAGATGATTCGATTCCCTGATGTTGACACTTCAATTTCCA 51 −1.178321338 −1 Stayer CTGTACCCCATTTCTTCCCACGTATTCCTCGAGGAAGGTTAGCCCTGAGCTAACATCTGC 52 −1.3986266 −1 Stayer CTGTACCCCATTTCTTCCCACGTATTCCTCGAAACTAGGAAATTAACATTAGTATAGTAC 53 −1.2344099 −1 Stayer CTGTACCCCATTTCTTCCCACGTATTCCTCGAGCCCAACGTTTTTTATTGACAAGTAATT 54 −1.300138442 −1 Stayer CTGTACCCCATTTCTTCCCACGTATTCCTCGATGGTCAGAGAGTTCTGAGCATGTTTGCA 55 −1.152917744 −1 Stayer GATGGCCAATAAACACTTGAAAAGGTACTCGATTTGCCAATATTTTGCTGAGGATTTTTC 56 −1.279814722 −1 Stayer TCTTTATATTGAGGTTCTAGCTTGTGATTCGAGAAGGAGACCTTGGTTATTTATTCTTAC 57 −1.549522786 −1 Stayer TGGTACTTACTCATTTGATATCTGCCCGTCGAATGCAAACTATGCCATTCTCCACTACAA 58 −1.620917244 −1 Stayer TGGTACTTACTCATTTGATATCTGCCCGTCGAAGACATGGATATATAAATATATGTTTTC 59 −1.250486699 −1 Stayer ATGCAAAAATTCTCAAAATTTTGGCAACTCGACGGGCAGATATCAAATGAGTAAGTACCA 60 −1.542378091 −1 Stayer TGGTACTTACTCATTTGATATCTGCCCGTCGATCTAAGCAGAAAACACGAAGAAACATAA 61 −1.310427896 −1 Stayer ATATTAACAGCAAACCCTTAGTGGGTACTCGAAGCTCCCTAAGATTAGGAACCTTGTCTT 62 −1.595397371 −1 Stayer ATATTAACAGCAAACCCTTAGTGGGTACTCGAGGGTACTGAGTTGCAGACAGGTTAATGG 63 −1.315228289 −1 Stayer ATATTAACAGCAAACCCTTAGTGGGTACTCGAAGAAAGTAAAACAAATGGAGAGAAGTGT 64 −1.197102917 −1 Stayer TCAAAGTCCCGTTCAACTGTACATTTCTTCGAGTTATATCAGCCACTAACTAACAAAAAT

TABLE 33.a5 Probe Location 4 kb Sequence Location N Chr Start1 End1 Start2 End2 Chr Start1 End1 Start2 1 6 47915416 47915447 48137538 48137569 6 47915416 47919417 48133568 2 11 36333514 36333545 36350786 36350817 11 36333514 36337515 36350786 3 11 36333514 36333545 36436048 36436079 11 36333514 36337515 36436048 4 11 36333514 36333545 36552325 36552356 11 36333514 36337515 36548355 5 11 36448245 36448276 36631315 36631346 11 36444275 36448276 36627345 6 8 11863063 11863094 11908667 11908698 8 11863063 11867064 11908667 7 5 17680263 17680294 17812085 17812116 5 17676293 17680294 17812085 8 5 17680263 17680294 17962676 17962707 5 17676293 17680294 17958706 9 5 17680263 17680294 17952666 17952697 5 17676293 17680294 17952666 10 4 84046655 84046686 84262207 84262238 4 84042685 84046686 84262207 11 4 84093825 84093856 84262207 84262238 4 84089855 84093856 84262207 12 5 13718587 13718618 13770118 13770149 5 13714617 13718618 13770118 13 5 13716369 13716400 13770118 13770149 5 13716369 13720370 13770118 14 14 59182856 59182887 59248524 59248555 14 59178886 59182887 59244554 15 14 59182856 59182887 59237657 59237688 14 59178886 59182887 59237657 16 5 35820030 35820061 35852447 35852478 5 35820030 35824031 35848477 17 5 35820030 35820061 35866091 35866122 5 35820030 35824031 35866091 18 5 35852447 35852478 35900637 35900668 5 35848477 35852478 35900637 19 11 20175502 20175533 20248248 20248279 11 20175502 20179503 20244278 20 11 20175502 20175533 20322464 20322495 11 20175502 20179503 20318494 21 11 20248248 20248279 20281555 20281586 11 20244278 20248279 20281555 22 20 24605232 24605263 24706408 24706439 20 24601262 24605263 24706408 23 20 32536895 32536926 32592625 32592656 20 32536895 32540896 32588655 24 20 32570542 32570573 32598309 32598340 20 32570542 32574543 32594339 25 20 32570542 32570573 32598340 32598371 20 32570542 32574543 32598340 26 20 32570542 32570573 32675890 32675921 20 32570542 32574543 32671920 27 20 32592625 32592656 32722678 32722709 20 32588655 32592656 32718708 28 20 32598340 32598371 32645786 32645817 20 32598340 32602341 32645786 29 11 26122948 26122979 26187791 26187822 11 26122948 26126949 26183821 30 11 26122948 26122979 26192170 26192201 11 26122948 26126949 26188200 31 16 33352821 33352852 33654217 33654248 16 33352821 33356822 33650247 32 16 33410233 33410264 33654217 33654248 16 33410233 33414234 33650247 33 16 33479236 33479267 33654217 33654248 16 33479236 33483237 33650247 34 16 33563090 33563121 33654217 33654248 16 33563090 33567091 33650247 35 16 33622760 33622791 33654217 33654248 16 33622760 33626761 33650247 36 16 33654217 33654248 33706816 33706847 16 33650247 33654248 33702846 37 16 33654217 33654248 33733451 33733482 16 33650247 33654248 33729481 38 16 33654217 33654248 33741064 33741095 16 33650247 33654248 33737094 39 16 33654217 33654248 33733482 33733513 16 33650247 33654248 33733482 40 16 33654217 33654248 33760460 33760491 16 33650247 33654248 33756490 41 16 33654217 33654248 33760582 33760613 16 33650247 33654248 33760582 42 16 33654217 33654248 33768286 33768317 16 33650247 33654248 33768286 43 16 33654217 33654248 33815034 33815065 16 33650247 33654248 33815034 44 16 33654217 33654248 33852194 33852225 16 33650247 33654248 33848224 45 29 17033576 17033607 17155847 17155878 29 17033576 17037577 17151877 46 29 17048693 17048724 17144042 17144073 29 17048693 17052694 17144042 47 29 17144042 17144073 17262741 17262772 29 17144042 17148043 17262741 48 29 17144042 17144073 17336437 17336468 29 17144042 17148043 17332467 49 29 17144042 17144073 17332733 17332764 29 17144042 17148043 17332733 50 29 17286082 17286113 17357582 17357613 29 17286082 17290083 17353612 51 1 61392274 61392305 61544818 61544849 1 61388304 61392305 61540848 52 1 61392274 61392305 61577443 61577474 1 61388304 61392305 61573473 53 1 61392274 61392305 61570715 61570746 1 61388304 61392305 61570715 54 1 61392274 61392305 61578119 61578150 1 61388304 61392305 61578119 55 13 4269642 4269673 4440946 4440977 13 4269642 4273643 4440946 56 27 25376884 25376915 25471835 25471866 27 25376884 25380885 25471835 57 1 145659771 145659802 145699582 145699613 1 145659771 145663772 145699582 58 1 145659771 145659802 145762480 145762511 1 145659771 145663772 145762480 59 1 145659771 145659802 145800266 145800297 1 145659771 145663772 145796296 60 1 145659771 145659802 145793388 145793419 1 145659771 145663772 145793388 61 13 19942675 19942706 20034761 20034792 13 19942675 19946676 20030791 62 13 20002320 20002351 20034761 20034792 13 20002320 20006321 20030791 63 13 20007058 20007089 20034761 20034792 13 20007058 20011059 20030791 64 5 52200069 52200100 52330760 52330791 5 52196099 52200100 52326790

TABLE 33.a6 4 kb Sequence Location N End2 Probe Primer ID-1 1 48137569 ABCC9_6_47915416_47925286_48134697_48137569_RF OBD RD043.001 2 36354787 ACACA_11_36333514_36339214_36350786_36357493_RR OBD RD043.005 3 36440049 ACACA_11_36333514_36339214_36436048_36448276_RR OBD RD043.009 4 36552356 ACACA_11_36333514_36339214_36541652_36552356_RF OBD RD043.013 5 36631346 ACACA_11_36436048_36448276_36626441_36631346_FF OBD RD043.017 6 11912668 ACACB_8_11863063_11867350_11908667_11911946_RR OBD RD043.021 7 17816086 ACBD6_5_17677182_17680294_17812085_17822701_FR OBD RD043.025 8 17962707 ACBD6_5_17677182_17680294_17952666_17962707_FF OBD RD043.029 9 17956667 ACBD6_5_17677182_17680294_17952666_17962707_FR OBD RD043.033 10 84266208 AHCYL2_4_84035626_84046686_84262207_84266431_FR OBD RD043.037 11 84266208 AHCYL2_4_84081753_84093856_84262207_84266431_FR OBD RD043.041 12 13774119 ANGPTL1_5_13716369_13718618_13770118_13781369_FR OBD RD043.045 13 13774119 ANGPTL1_5_13716369_13718618_13770118_13781369_RR OBD RD043.049 14 59248555 APC_14_59179179_59182887_59237657_59248555_FF OBD RD043.053 15 59241658 APC_14_59179179_59182887_59237657_59248555_FR OBD RD043.057 16 35852478 APOA2_5_35820030_35830912_35848600_35852478_RF OBD RD043.061 17 35870092 APOA2_5_35820030_35830912_35866091_35873759_RR OBD RD043.065 18 35904638 APOA2_5_35848600_35852478_35900637_35912475_FR OBD RD043.069 19 20248279 BECN1_11_20175502_20184049_20243179_20248279_RF OBD RD043.073 20 20322495 BECN1_11_20175502_20184049_20320840_20322495_RF OBD RD043.077 21 20285556 BECN1_11_20243179_20248279_20281555_20289129_FR OBD RD043.081 22 24710409 BTN1A1_20_24591764_24605263_24706408_24710466_F R OBD RD043.085 23 32592656 BTNL2_20_32536895_32543196_32585002_32592656_RF OBD RD043.089 24 32598340 BTNL2_20_32570542_32582104_32597196_32598340_RF OBD RD043.093 25 32602341 BTNL2_20_32570542_32582104_32598340_32606017_RR OBD RD043.097 26 32675921 BTNL2_20_32570542_32582104_32672903_32675921_RF OBD RD043.101 27 32722709 BTNL2_20_32585002_32592656_32716550_32722709_FF OBD RD043.105 28 32649787 BTNL2_20_32598340_32606017_32645786_32652591_RR OBD RD043.109 29 26187822 CACNA1G_11_26122948_26135515_26185131_26187822_RF OBD RD043.113 30 26192201 CACNA1G_11_26122948_26135515_26187822_26192201_RF OBD RD043.117 31 33654248 CACNA2D3_16_33352821_33354631_33641948_33654248_RF OBD RD043.121 32 33654248 CACNA2D3_16_33410233_33413906_33641948_33654248_RF OBD RD043.125 33 33654248 CACNA2D3_16_33479236_33480664_33641948_33654248_RF OBD RD043.129 34 33654248 CACNA2D3_16_33563090_33565331_33641948_33654248_RF OBD RD043.133 35 33654248 CACNA2D3_16_33622760_33627636_33641948_33654248_RF OBD RD043.137 36 33706847 CACNA2D3_16_33641948_33654248_33704852_33706847_FF OBD RD043.141 37 33733482 CACNA2D3_16_33641948_33654248_33729470_33733482_FF OBD RD043.145 38 33741095 CACNA2D3_16_33641948_33654248_33733482_33741095_FF OBD RD043.149 39 33737483 CACNA2D3_16_33641948_33654248_33733482_33741095_FR OBD RD043.153 40 33760491 CACNA2D3_16_33641948_33654248_33757281_33760491_FF OBD RD043.157 41 33764583 CACNA2D3_16_33641948_33654248_33760582_33768051_FR OBD RD043.161 42 33772287 CACNA2D3_16_33641948_33654248_33768286_33770169_FR OBD RD043.165 43 33819035 CACNA2D3_16_33641948_33654248_33815034_33817501_FR OBD RD043.169 44 33852225 CACNA2D3_16_33641948_33654248_33848517_33852225_FF OBD RD043.173 45 17155878 CACNB2_29_17033576_17046068_17154781_17155878_RF OBD RD043.177 46 17148043 CACN_B2_29_17048693_17053442_17144042_17154089_RR OBD RD043.181 47 17266742 CACNB2_29_17144042_17154089_17262741_17269092_RR OBD RD043.185 48 17336468 CACNB2_29_17144042_17154089_17332733_17336468_RF OBD RD043.189 49 17336734 CACNB2_29_17144042_17154089_17332733_17336468_RR OBD RD043.193 50 17357613 CACNB2_29_17286082_17289972_17348926_17357613_RF OBD RD043.197 51 61544849 CAMK2G_1_61385709_61392305_61537867_61544849_FF OBD RD043.201 52 61577474 CAMK2G_1_61385709_61392305_61570715_61577474_FF OBD RD043.205 53 61574716 CAMK2G_1_61385709_61392305_61570715_61577474_FR OBD RD043.209 54 61582120 CAMK2G_1_61385709_61392305_61578119_61589600_FR OBD RD043.213 55 4444947 CARD11_13_4269642_4272623_4440946_4446573_RR OBD RD043.217 56 25475836 CASP3_27_25376884_25380938_25471835_25478467_RR OBD RD043.221 57 145703583 CCNDBP1_1_145659771_145664399_145699582_145711153_RR OBD RD043.225 58 145766481 CCNDBP1_1_145659771_145664399_145762480_145771097_RR OBD RD043.229 59 145800297 CCNDBP1_1_145659771_145664399_145793388_145800297_RF OBD RD043.233 60 145797389 CCNDBP1_1_145659771_145664399_145793388_145800297_RR OBD RD043.237 61 20034792 CD19_13_19942675_19947695_20028912_20034792_RF OBD RD043.241 62 20034792 CD19_13_20002320_20006400_20028912_20034792_RF OBD RD043.245 63 20034792 CD19_13_20007058_20010478_20028912_20034792_RF OBD RD043.249 64 52330791 CD2_5_52197323_52200100_52321910_52330791_FF OBD RD043.253

TABLE 33.a7 N Primer Sequence Primer ID-2 Primer Sequence 1 CTGGGAATACTTATGATTTGGCGACC OBD RD043.003 TCCTTGTGACCTATTGGACTGAGGGC 2 GCAGATTAGAAAGGAGTCATCAGAAA OBD RD043.007 CCTGATTCTAAACAGCATTCTGGGAG 3 CCAACTCTGTCGCTTGTTACACTTAG OBD RD043.011 ACTCTTTACCCTGTGGTGTGGACGGT 4 CAGTTCACGGAAATGTCCCCAGAGCA OBD RD043.015 CCAACTCTGTCGCTTGTTACACTTAG 5 CCAACTCTGTCGCTTGTTACACTTAG OBD RD043.019 GCACAACAATGGAGTGACCCACAGCA 6 GGAGAGCCACCCTGGATACACAG OBD RD043.023 CCGACAAAGGGCAGAGGTGAGAT 7 CGGATTTTAGAGTTGATAAGCACACC OBD RD043.027 CACCAGGTTTTCCCCTTCAGTGTGAC 8 CGGATTTTAGAGTTGATAAGCACACC OBD RD043.031 GACCGATTTGAGGTGCTTACGGATGG 9 CGGATTTTAGAGTTGATAAGCACACC OBD RD043.035 GCTGGGTCACCACGCATAGGATGA 10 GCAGCAGAGTATCATTCTTGCCCTC OBD RD043.039 AGGGCAGAGGGCTATGGGTGCTT 11 CGTCTGAGGAAAGTGCCAGGAAAG OBD RD043.043 AGGGCAGAGGGCTATGGGTGCTT 12 TGCTAAACAACCACTGGACCACTGGG OBD RD043.047 ATGGATGGCTCTGTCAACTTCTTCAG 13 CGGGCAAAGGTCTAACAGAAGCAGGA OBD RD043.051 ATGGATGGCTCTGTCAACTTCTTCAG 14 CTCCTCTGGACTCCTATTTCTGGGCA OBD RD043.055 CACTTGGAGCGGTTTTGTTCACACTT 15 CTCCTCTGGACTCCTATTTCTGGGCA OBD RD043.059 GATGGCAGCATAGTAACAGTTCTACA 16 CACTTCCTTCAGAAAGCGGGTGCTCA OBD RD043.063 GAACAACTGCTCCAACACAAACAAGC 17 TGGGAGGAACCAGGTGGGTAACG OBD RD043.067 TTCCCCTCCTCTCCATTGGGTCA 18 TGGGAGGAACCAGGTGGGTAACG OBD RD043.071 CTTCCTTCAGAAAGCGGGTGCTC 19 GTCGCCAGGTTCCGTTCTTGGTG OBD RD043.075 GACTGAGCATTATGGAGGCAGCC 20 TGTGGGCTTGTTCTTACTTCCTGAAT OBD RD043.079 TCCATCTTGGGTCCCTTCTCCATCCT 21 AAGCAACAGTGGTGGAGGAGACC OBD RD043.083 TTGGGTCCCTTCTCCATCCTGCC 22 GGTTAGGGAGTGCTATGAGGGAG OBD RD043.087 GCCCTCGGTGTAGTCCTTGCTGT 23 TACACTTTGGGAGTTTGTCTTTGAAG OBD RD043.091 ACTTGAAGACAGAACTGCTTTGACAA 24 CACTATGGAAAACAGTATGGAGAT OBD RD043.095 TCTGAGATGTCCTTCTTGATTCATA 25 TACACTTTGGGAGTTTGTCTTTGAAG OBD RD043.099 CACCTGCGTAGATTTGTGTAACCACG 26 TCTGATAGGGCTTGTGATTTTATTT OBD RD043.103 ACTATGGAAAACAGTATGGAGATTT 27 GTCTTTCCCTATGTCAACCTTGTGT OBD RD043.107 GCCACTATGGAAAACAGTATGGAGAT 28 TCTTCACCTTAGTCTCCTTATCTCTA OBD RD043.111 GGACTCAGGGCTCATCTCTCATTTGT 29 CCACCAGTGCCACGAGAACCTCT OBD RD043.115 CCCAAAGGTCCAGAGCGGAGAAA 30 CAGGGCTGCTTGAATGGAAAGGG OBD RD043.119 CAACCCAAAGGTCCAGAGCGGAG 31 GGGCAGCCAGAAAGCACACAGTT OBD RD043.123 CCCTTGTGACCTCCTACTCTGCC 32 AACCCAATCCAGGCAAGCCACCC OBD RD043.127 GCTGAAGTTGACCTTGTCTCCGC 33 GGGCAGCCAGAAAGCACACAGTT OBD RD043.131 ATTCGGTGGGTCTGGAGAGAGGC 34 GGGCAGCCAGAAAGCACACAGTT OBD RD043.135 GGGAGGAGAAGCAGAGCACACAG 35 GGGCAGCCAGAAAGCACACAGTT OBD RD043.139 GGAGGCTGATGTCTGTCCTTGGG 36 GGGCAGCCAGAAAGCACACAGTT OBD RD043.143 CCCGCTGCTCTCAACAGACACTG 37 TCCATTTTCCCCATCTCTCACCCTCC OBD RD043.147 ATGAGAACCAAGGTCAGGGAGGTAAA 38 TCCATTTTCCCCATCTCTCACCCTCC OBD RD043.151 CCCACTCTCTTTGAAGGAAATCACAT 39 GGGCAGCCAGAAAGCACACAGTT OBD RD043.155 CCTCCACCATTCTCCTCCAGTCC 40 GGGCAGCCAGAAAGCACACAGTT OBD RD043.159 GGCAGGGTCATTGTGATGGTCCG 41 AACCCAATCCAGGCAAGCCACCC OBD RD043.163 CCTCCTATCATCTCTCTCCCCAC 42 GGGCAGCCAGAAAGCACACAGTT OBD RD043.167 AGTCTCCCCTCCCACTGTTGGCA 43 ATCCATTTTCCCCATCTCTCACCCTC OBD RD043.171 CTTAGACTCCAGTGGCTGAATGTCCA 44 GTTGGGCAGCCAGAAAGCACACAG OBD RD043.175 GAACTTCTCGTGGGACACCCTCA 45 GAGCAAAGTAGTCAGCCAGCCAGAAT OBD RD043.179 GTTCTTTTCCTGGTAGGTCATCCTGT 46 AAACCTGTGCGGGCTGTCTGACCA OBD RD043.183 GCCTGAACCCACTTAGATAATGTGTG 47 TCCCGCTCCCTGTTTTCCACCAT OBD RD043.187 CACTGTGGCACTGGGAGGAAACG 48 GCCTGAACCCACTTAGATAATGTGTG OBD RD043.191 GTTCCTGTGGTTGGTTGGTTGGGATG 49 CCTGGGTAGATGAGCCTGTAGCC OBD RD043.195 TCCCGCTCCCTGTTTTCCACCAT 50 CCCTCGCCTCCTATTCCTATGGC OBD RD043.199 CCCATCCCTTTCAGCCTCACTCA 51 CCACGCCATTTAGGACTCGGGTC OBD RD043.203 GGGTCAGTCTTCCGCAGCACAAA 52 TATGGGATTTCTTTGGTAGGGACG OBD RD043.207 TCAGTCAATACATACAGTTCATACT 53 GCCCAACCTCTGTGTTCCCATTC OBD RD043.211 TCCACGGTTCAGGCATCCACTGG 54 GCCCAACCTCTGTGTTCCCATTC OBD RD043.215 CCCCGAAGGCAGGCTATGGAGAA 55 GAACAGGTGGCTCACAAAGGAGGATA OBD RD043.219 GACAAGGACAACACAAAGAAGGAAAA 56 GCTCCAGTTTGCTGAACCAACCC OBD RD043.223 AGAGCGTCCCTGGAAAGTGGCAG 57 GGCACCCCTTATCAGAGACCAGC OBD RD043.227 TTGGGCAGAGGAGAAGAGTGTGC 58 GGCACCCCTTATCAGAGACCAGC OBD RD043.231 GGCATCTCCTCTTCTGCTCACAC 59 CCAAAACCTGACAAGCACAGCAT OBD RD043.235 GAGACAGGTGGATGGCGATGGTA 60 GGCACCCCTTATCAGAGACCAGC OBD RD043.239 CCTCCATCTCTGCCACTCAGGAA 61 GACCTTCATCCGAGCCTCCGTTT OBD RD043.243 TGCCTCTCCTGCCTCTGTCTCAC 62 GAGACCTTCATCCGAGCCTCCGT OBD RD043.247 GGGCGAACAGCAAGAGACAAGCA 63 GACCTTCATCCGAGCCTCCGTTT OBD RD043.251 CCCTGGATGTGTGACCTTCGGCA 64 ATCCAAACCATTGAAACCCTGGGC OBD RD043.255 GATTGAGACTTGCGTTTTGAGGGC

TABLE 33.a8 N Probe Marker 1 ABCC9 OBD RD043.001.003 2 ACACA OBD RD043.005.007 3 ACACA OBD RD043.009.011 4 ACACA OBD RD043.013.015 5 ACACA OBD RD043.017.019 6 ACACB OBD RD043.021.023 7 ACBD6 OBD RD043.025.027 8 ACBD6 OBD RD043.029.031 9 ACBD6 OBD RD043.033.035 10 AHCYL2 OBD RD043.037.039 11 AHCYL2 OBD RD043.041.043 12 ANGPTL1 OBD RD043.045.047 13 ANGPTL1 OBD RD043.049.051 14 APC OBD RD043.053.055 15 APC OBD RD043.057.059 16 APOA2 OBD RD043.061.063 17 APOA2 OBD RD043.065.067 18 APOA2 OBD RD043.069.071 19 BECN1 OBD RD043.073.075 20 BECN1 OBD RD043.077.079 21 BECN1 OBD RD043.081.083 22 BTN1A1 OBD RD043.085.087 23 BTNL2 OBD RD043.089.091 24 BTNL2 OBD RD043.093.095 25 BTNL2 OBD RD043.097.099 26 BTNL2 OBD RD043.101.103 27 BTNL2 OBD RD043.105.107 28 BTNL2 OBD RD043.109.111 29 CACNA1G OBD RD043.113.115 30 CACNA1G OBD RD043.117.119 31 CACNA2D3 OBD RD043.121.123 32 CACNA2D3 OBD RD043.125.127 33 CACNA2D3 OBD RD043.129.131 34 CACNA2D3 OBD RD043.133.135 35 CACNA2D3 OBD RD043.137.139 36 CACNA2D3 OBD RD043.141.143 37 CACNA2D3 OBD RD043.145.147 38 CACNA2D3 OBD RD043.149.151 39 CACNA2D3 OBD RD043.153.155 40 CACNA2D3 OBD RD043.157.159 41 CACNA2D3 OBD RD043.161.163 42 CACNA2D3 OBD RD043.165.167 43 CACNA2D3 OBD RD043.169.171 44 CACNA2D3 OBD RD043.173.175 45 CACNB2 OBD RD043.177.179 46 CACNB2 OBD RD043.181.183 47 CACNB2 OBD RD043.185.187 48 CACNB2 OBD RD043.189.191 49 CACNB2 OBD RD043.193.195 50 CACNB2 OBD RD043.197.199 51 CAMK2G OBD RD043.201.203 52 CAMK2G OBD RD043.205.207 53 CAMK2G OBD RD043.209.211 54 CAMK2G OBD RD043.213.215 55 CARD11 OBD RD043.217.219 56 CASP3 OBD RD043.221.223 57 CCNDBP1 OBD RD043.225.227 58 CCNDBP1 OBD RD043.229.231 59 CCNDBP1 OBD RD043.233.235 60 CCNDBP1 OBD RD043.237.239 61 CD19 OBD RD043.241.243 62 CD19 OBD RD043.245.247 63 CD19 OBD RD043.249.251 64 CD2 OBD RD043.253.255

TABLE 33.b1 N Probe GeneLocus Probe_Count_Total Probe_Count_Sig 65 CD226_8_85390137_85395670_85431393_85435046_RR CD226 1 31 66 CD40_22_34955976_34961456_35003447_35009473_FF CD40 1 30 67 CD5_12_20785118_20787274_20916990_20922807_RF CD5 2 31 68 CD5_12_20843696_20847942_20916990_20922807_RF CD5 2 31 69 CDH1_3_18955128_18959809_19065895_19074313_FF CDH1 1 28 70 CERK_28_42579274_42585201_42607249_42612447_RR CERK 1 31 71 CHL1_16_15145284_15151298_15196227_15203340_FF CHL1 6 73 72 CHL1_16_15145284_15151298_15255076_15264032_FF CHL1 6 73 73 CHL1_16_15145284_15151298_15255076_15264032_FR CHL1 6 73 74 CHL1_16_15145284_15151298_15301390_15310795_FR CHL1 6 73 75 CHL1_16_15145284_15151298_15326701_15332680_FF CHL1 6 73 76 CHL1_16_15165960_15173124_15233430_15239181_RF CHL1 6 73 77 CHRDL2_7_69179023_69184961_69220436_69225536_RF CHRDL2 2 61 78 CHRDL2_7_69220436_69225536_69328532_69336827_FR CHRDL2 2 61 79 CHST10_15_8874159_8888709_8973363_8982576_FR CHST10 3 64 80 CHST10_15_8874159_8888709_9029805_9032751_FF CHST10 3 64 81 CHST10_15_8936185_8939355_8973363_8982576_RR CHST10 3 64 82 COL15A1_25_5777848_5781338_5838527_5844153_RR COL15A1 1 31 83 COL18A1_26_40666594_40668538_40680588_40685271_RR COL18A1 1 30 84 COL4A4_6_15299757_15310450_15375645_15378009_RF COL4A4 2 48 85 COL4A4_6_15436171_15443495_15487479_15493934_FR COL4A4 2 48 86 CREBBP_13_38904201_38905631_39179236_39195594_RF CREBBP 7 139 87 CREBBP_13_38931046_38933583_39179236_39195594_RF CREBBP 7 139 88 CREBBP_13_38974958_38977634_39179236_39195594_RF CREBBP 7 139 89 CREBBP_13_38981963_38985123_39179236_39195594_RF CREBBP 7 139 90 CREBBP_13_38999154_39003472_39179236_39195594_RF CREBBP 7 139 91 CREBBP_13_39073684_39080240_39179236_39195594_RF CREBBP 7 139 92 CREBBP_13_39112330_39113797_39179236_39195594_RF CREBBP 7 139 93 CRP_5_37768331_37775673_37803790_37809028_RF CRP 3 33 94 CRP_5_37768331_37775673_37803790_37809028_RR CRP 3 33 95 CRP_5_37768331_37775673_37834953_37842330_RR CRP 3 33 96 CTLA4_18_78522827_78530189_78600391_78604267_FR CTLA4 1 29 97 DDIT3_6_75012399_75018811_75092742_75096887_RR DDIT3 2 23 98 DDIT3_6_75012399_75018811_75098342_75106967_RR DDIT3 2 23 99 DGKH_17_27888277_27893919_27983597_27991700_RR DGKH 4 168 100 DGKH_17_27888277_27893919_28023161_28030553_RR DGKH 4 168 101 DGKH_17_27888277_27893919_28087062_28095320_RR DGKH 4 168 102 DGKH_17_27983597_27991700_28038960_28044643_FF DGKH 4 168 103 DIAPH3_17_35244506_35247777_35523297_35543766_RR DIAPH3 2 250 104 DIAPH3_17_35550338_35555886_35584820_35594304_FR DIAPH3 2 250 105 DLK1_24_42596087_42597712_42651466_42656554_FF DLK1 1 31 106 DOK5_22_41633839_41639527_41876029_41882809_RF DOK5 2 31 107 DOK5_22_41845220_41849884_41876029_41882809_RF DOK5 2 31 108 ETS1_7_37223720_37228234_37244778_37252642_RR ETS1 1 56 109 GABPA_26_23335158_23338855_23360793_23370765_RR GABPA 1 91 110 GJA5_5_48248931_48256193_48407852_48413621_FR GJA5 5 88 111 GJA5_5_48248931_48256193_48407852_48413621_RR GJA5 5 88 112 GJA5_5_48256193_48265184_48407852_48413621_FR GJA5 5 88 113 GJA5_5_48297725_48306379_48407852_48413621_FR GJA5 5 88 114 GJA5_5_48370294_48376643_48407852_48413621_RR GJA5 5 88 115 GPC5_17_62030628_62037968_62292109_62298602_FR GPC5 2 249 116 GPC5_17_62161244_62167825_62292109_62298602_FR GPC5 2 249 117 GRK5_1_13009800_13016170_13161461_13167914_FR GRK5 3 31 118 GRK5_1_13009800_13016170_13204085_13213606_FF GRK5 3 31 119 GRK5_1_13135627_13139975_13204085_13213606_FF GRK5 3 31 120 GSK3B_19_38827199_38835574_39055705_39060019_RR GSK3B 1 132 121 HDAC3_14_35404443_35406152_35458546_35471150_RR HDAC3 1 104 122 HDAC5_11_19330735_19336727_19434549_19441692_RR HDAC5 2 30 123 HDAC5_11_19372111_19379011_19491838_19494990_FF HDAC5 2 30 124 HDAC9_4_51008167_51021720_51107519_51111219_RF HDAC9 1 280 125 HOXC6_6_70794688_70801196_70818032_70820676_RF HOXC6 1 31 126 HSDL2_25_17089584_17093930_17167460_17175476_FF HSDL2 3 102 127 HSDL2_25_17089584_17093930_17167460_17175476_FR HSDL2 3 102 128 HSDL2_25_17089584_17093930_17197980_17209878_FF HSDL2 3 102

TABLE 33.b2 N HyperG_Stats FDR_HyperG Percent_Sig logFC AveExpr 65 0.198752749 0.267074007 3.23 0.341840161 7.247636443 66 0.193928419 0.267074007 3.33 −0.178317344 10.69384186 67 0.024599258 0.075554863 6.45 −0.242153231 10.73889105 68 0.024599258 0.075554863 6.45 −0.260248811 11.120971 69 0.183998999 0.267074007 3.57 −0.282497053 11.11483854 70 0.198752749 0.267074007 3.23 −0.448599336 8.889809603 71 0.0000287855939384343 0.000742668 8.22 0.462470187 8.5481053 72 0.0000287855939384343 0.000742668 8.22 0.410028111 8.628990709 73 0.0000287855939384343 0.000742668 8.22 0.445873686 8.369941593 74 0.0000287855939384343 0.000742668 8.22 0.413519891 8.631292888 75 0.0000287855939384343 0.000742668 8.22 0.451423499 8.55317371 76 0.0000287855939384343 0.000742668 8.22 −0.251896305 6.606225387 77 0.075709775 0.157525178 3.28 0.284071373 7.894826629 78 0.075709775 0.157525178 3.28 0.298147218 7.7720811 79 0.013845037 0.064041001 4.69 −0.409059439 7.708930887 80 0.013845037 0.064041001 4.69 −0.25346967 8.649906865 81 0.013845037 0.064041001 4.69 0.252289513 8.203650527 82 0.198752749 0.267074007 3.23 −0.638663316 8.462246587 83 0.193928419 0.267074007 3.33 −0.691447546 9.504132323 84 0.051914218 0.131312433 4.17 0.26396571 9.117422855 85 0.051914218 0.131312433 4.17 0.357277506 7.749299691 86 0.000137621 0.002219133 5.04 −0.489675835 8.316954487 87 0.000137621 0.002219133 5.04 −0.59449685 8.143398203 88 0.000137621 0.002219133 5.04 −0.258158385 9.427438624 89 0.000137621 0.002219133 5.04 −0.542091889 7.809236934 90 0.000137621 0.002219133 5.04 −0.570549519 8.272773989 91 0.000137621 0.002219133 5.04 −0.519347042 8.352346785 92 0.000137621 0.002219133 5.04 −0.474046419 8.086674809 93 0.002335573 0.01673827 9.09 0.225177272 9.290490657 94 0.002335573 0.01673827 9.09 0.257141717 10.68770958 95 0.002335573 0.01673827 9.09 0.225607706 10.55701332 96 0.189010904 0.267074007 3.45 0.244602905 8.422577617 97 0.014290491 0.064041001 8.7 0.215926084 10.1135098 98 0.014290491 0.064041001 8.7 0.413805259 9.019249379 99 0.037378088 0.104821159 2.38 0.406030868 7.865506845 100 0.037378088 0.104821159 2.38 0.335540786 8.434376341 101 0.037378088 0.104821159 2.38 0.268362014 8.83590478 102 0.037378088 0.104821159 2.38 −0.1949879 9.068498407 103 0.272436907 0.310300562 0.8 1.177347719 8.350585003 104 0.272436907 0.310300562 0.8 0.198636698 10.37949827 105 0.198752749 0.267074007 3.23 −0.400257671 9.279193522 106 0.024599258 0.075554863 6.45 −0.255902452 11.31369569 107 0.024599258 0.075554863 6.45 −0.197532334 11.33660679 108 0.292341721 0.325104155 1.79 −0.325806823 7.500438844 109 0.356204452 0.369972517 1.1 −1.140777936 8.452195491 110 0.00071906 0.009275877 5.68 −0.415749473 11.59733518 111 0.00071906 0.009275877 5.68 −0.307210255 11.22897697 112 0.00071906 0.009275877 5.68 −0.383777265 9.880520247 113 0.00071906 0.009275877 5.68 −0.367375654 10.47600421 114 0.00071906 0.009275877 5.68 −0.418188826 11.1638961 115 0.272492977 0.310300562 0.8 0.312761226 8.158780766 116 0.272492977 0.310300562 0.8 0.218475376 9.612836388 117 0.001955877 0.014841655 9.68 −0.376092453 10.23852086 118 0.001955877 0.014841655 9.68 −0.346076177 10.08178634 119 0.001955877 0.014841655 9.68 −0.19700025 11.98270597 120 0.368643954 0.369972517 0.76 0.236007177 7.969612712 121 0.365777771 0.369972517 0.96 −0.318530813 7.005872794 122 0.023201487 0.075554863 6.67 −0.567555056 9.695872092 123 0.023201487 0.075554863 6.67 −0.311003579 8.846166998 124 0.230471214 0.297307866 0.36 0.267534336 7.807343578 125 0.198752749 0.267074007 3.23 −0.284488126 10.50098524 126 0.04181789 0.112385579 2.94 0.409504025 8.955642386 127 0.04181789 0.112385579 2.94 0.275378575 9.43472352 128 0.04181789 0.112385579 2.94 0.37672213 9.562492703

TABLE 33.b3 N t P.Value adj.P.Val B FC 65 5.618655797 0.0000199272532249328 0.003966133 2.970358272 1.2673721 66 −5.10596284 0.0000617052113463042 0.008329136 1.895072775 0.883733119 67 −5.936420225 0.0000100379326708335 0.002463079 3.620955306 0.845482482 68 −6.14157352 0.00000648983188875642 0.001782876 4.03379312 0.834943911 69 −7.909652841 0.000000190517352509565 0.000176954 7.332040725 0.822166758 70 −7.419021619 0.000000486229190399068 0.000327031 6.464905236 0.732753909 71 6.686410206 0.00000209248781498571 0.000822758 5.100834912 1.377899042 72 5.428175718 0.0000302276235200180 0.005000177 2.574299106 1.328711704 73 6.52733514 0.00000290021776169651 0.001037747 4.793822411 1.362138768 74 5.554618228 0.0000229132183097780 0.004269944 2.83769231 1.331931503 75 5.455049104 0.0000284949740889623 0.004832995 2.630436111 1.367388786 76 −5.621056707 0.0000198233899082524 0.003965695 2.975322416 0.839791852 77 4.983263565 0.0000811872515612103 0.009898247 1.633703508 1.217626256 78 5.44278257 0.0000292728922433219 0.004943444 2.604822343 1.22956433 79 −5.983309313 0.00000908136757827868 0.002361761 3.715824347 0.753114204 80 −5.190006848 0.0000511739465631575 0.007206844 2.073279303 0.838876496 81 5.71974371 0.0000160008558050293 0.003467741 3.178744012 1.191095848 82 −6.403087538 0.00000375123437915977 0.001240133 4.551401529 0.642307783 83 −10.26896099 0.00000000322944539582748 0.00000854970466866222 11.00157549 0.619232224 84 6.538599393 0.00000283363426460291 0.001033085 4.815686956 1.200774887 85 8.497455807 0.0000000646633050589555 0.000078597025797400 8.322263656 1.281006243 86 −6.177261672 0.00000601894082752241 0.001701441 4.105008693 0.712185103 87 −5.47299969 0.0000273945059932764 0.004693558 2.66788725 0.662275388 88 −5.496015116 0.0000260468384551831 0.004515943 2.715850222 0.836154599 89 −6.291593561 0.00000473366295565049 0.001465557 4.331932541 0.686774373 90 −5.958739229 0.00000957033212471167 0.002438159 3.666149932 0.673360258 91 −7.020935167 0.00000106498214760689 0.000532857 5.733942795 0.697687533 92 −5.913971946 0.0000105319433085296 0.00255187 3.57543078 0.719942494 93 5.231815445 0.0000466369274249531 0.006813882 2.161666862 1.168920872 94 5.007912479 0.0000768248326803410 0.009606804 1.68631868 1.195108595 95 7.210365056 0.000000731398300322928 0.000419586 6.084829449 1.169269676 96 6.094643967 0.00000716734949527807 0.001955233 3.939871515 1.184766624 97 5.419098482 0.0000308369119963444 0.005054403 2.555318501 1.161449224 98 6.915832549 0.00000131460036416667 0.000596309 5.536873458 1.332194988 99 5.856598637 0.0000119111980213138 0.002765809 3.458771257 1.325035367 100 6.902941252 0.00000134913450281018 0.000598065 5.512585315 1.261850317 101 5.17067204 0.0000534219908481310 0.007416341 2.032343624 1.204439572 102 −5.2490489 0.0000448882307553045 0.006607886 2.198047673 0.873580223 103 5.956066197 0.00000962513428218130 0.002438159 3.660740777 2.261606163 104 5.540348785 0.0000236388142881637 0.004367942 2.808062497 1.147613384 105 −5.662792363 0.0000181039158418541 0.003741337 3.061500844 0.757722939 106 −5.516430295 0.0000249082421012251 0.004416684 2.758342073 0.83746311 107 −4.983217873 0.0000811955680862767 0.009898247 1.633605924 0.872040876 108 −8.393742068 0.0000000779901777084671 0.000084511023122425 8.151353285 0.797852065 109 −7.690570015 0.000000288337468652026 0.000248829 6.94943685 0.453514966 110 −8.767490453 0.0000000399545356666192 0.000064942768181451 8.759712775 0.749629965 111 −6.227343692 0.00000541666889080595 0.001588754 4.204641449 0.808203075 112 −6.509359957 0.00000300983019700269 0.001051643 4.75889243 0.766428298 113 −5.587701438 0.0000213173634345125 0.004137265 2.906293096 0.775191333 114 −6.963670287 0.00000119423299606347 0.00057037 5.626780498 0.748363538 115 5.331375489 0.0000374132338335943 0.005860047 2.371409711 1.242082693 116 5.387261614 0.0000330749297047718 0.005266339 2.488673122 1.163503359 117 −5.679474637 0.0000174600811226560 0.003701727 3.095886422 0.770521729 118 −7.010703269 0.00000108696808120982 0.000532857 5.714832403 0.786720904 119 −6.14332049 0.00000646592182931229 0.001782876 4.037283391 0.872362554 120 4.997714723 0.0000785999737756243 0.009703117 1.664557166 1.177728649 121 −5.976961259 0.00000920518649817264 0.002378108 3.702998116 0.801886073 122 −7.630840053 0.000000323183938483918 0.000262654 6.843838746 0.674759339 123 −5.872236016 0.0000115178359047956 0.002706691 3.490611042 0.806080832 124 5.079901556 0.0000654007694396312 0.008590182 1.839673798 1.20374878 125 −5.695385681 0.0000168678678005674 0.00361547 3.128649589 0.821032863 126 6.025225618 0.00000830560993803541 0.002174509 3.800377209 1.328229112 127 5.861408292 0.0000117887628752507 0.00275377 3.468567823 1.210311644 128 7.68141304 0.000000293415956096893 0.000248829 6.933283828 1.298388503

TABLE 33.b4 Loop Probe sequence N FC_1 LS Detected 60 mer 65 1.2673721 1 Sprinter ATTGAAATAAAAAAGTCAGTAGAAAAGATCGACAATAAAGACTATCAAGTATTGTACTAA 66 −1.131563341 −1 Stayer GCTGGGGCCATGTACATCCTGGGCACCATCGATAAGAAAACAAAATGCCTCAAAAGAAGT 67 −1.182756616 −1 Stayer GCCTTTCTCAAAACCCACTGTACACAGCTCGATTTTAATGGCTGCTTAATCTGAGTGGCT 68 −1.197685243 −1 Stayer GCCTTTCTCAAAACCCACTGTACACAGCTCGAGCCACCAGCTCATAAAGCCCCTGTGATC 69 −1.216298263 −1 Stayer TGAACAGTCAAGACTGGTGAGGAAGAATTCGAAGCCTATGCTGCCTTCCTGAAGCCTCCT 70 −1.364714658 −1 Stayer CGTGTACCTCACAGGGTTCTTCTAAAGATCGATGAGAACTTTTAAGATCTACTCTCTTAG 71 1.377899042 1 Sprinter ATTTCTTGACAGCGTGAATTCTTTACCCTCGAGCTAAAAATTTCACAAATAAACTCATAA 72 1.328711704 1 Sprinter ATTTCTTGACAGCGTGAATTCTTTACCCTCGATTATCTACTTGCAGATAACCTTTTTTCC 73 1.362138768 1 Sprinter ATTTCTTGACAGCGTGAATTCTTTACCCTCGAGGTACATAGAAGTACTAAAATACACAAA 74 1.331931503 1 Sprinter ATTTCTTGACAGCGTGAATTCTTTACCCTCGAGAGAAGTCAGAAGAATCTCTGGTTACTT 75 1.367388786 1 Sprinter ATTTCTTGACAGCGTGAATTCTTTACCCTCGATGATATTTATCTGTGTCATTTTTAATAG 76 −1.190771258 −1 Stayer ATTCAAAAACACACAAGTACTATTAAATTCGAATCCTTGCAAAAATTTCTCTTTTGTTTA 77 1.217626256 1 Sprinter AAAAAAATCTGTTCAGCTAATTTCTAACTCGACAAAGCTCTGTATTCTTTTTTTTAATTG 78 1.22956433 1 Sprinter AAAAAAATCTGTTCAGCTAATTTCTAACTCGAATAAAGGATGGTTGGAAAAAAAATAAAT 79 −1.327819863 −1 Stayer TACAGCTCAGATCAAATTGTTCTCAGAATCGATTGTATCCTGTTGGTCTATACTTCTGTC 80 −1.19207059 −1 Stayer TACAGCTCAGATCAAATTGTTCTCAGAATCGAAATGCACCAAGAAAAAGACTGCTATGTA 81 1.191095848 1 Sprinter TTAAGCACTTAATTTTTTTTTCTTGTGTTCGATTGTATCCTGTTGGTCTATACTTCTGTC 82 −1.556886007 −1 Stayer TCTCTCTAGAGCTCCACGGAGTTCGCAGTCGACTAATAAAGTAGCATCAAAATATATAAG 83 −1.614903039 −1 Stayer CTGTGCGTATGTACAATTGTTTTAATCCTCGACAGACGCGGTACCCGACCAGGTTGTCAC 84 1.200774887 1 Sprinter AGTTATTGACTCAACAAACATTATTGACTCGATGTACACTCTGGCTAGACCAGGGCAGGA 85 1.281006243 1 Sprinter GAGATATATACAGCATTTTTTCAGAAAATCGAGAGCAAAGAGACACTGGTTGAAATGAGA 86 −1.404129341 −1 Stayer TAAAGAAACGTCTATGAAAATTCAAAACTCGAAACACAATAATATTTGTATTTGGCTGTT 87 −1.509945889 −1 Stayer TAAAGAAACGTCTATGAAAATTCAAAACTCGAAGATATAATTCCACTACTTTTGGCTTCT 88 −1.195951086 −1 Stayer TAAAGAAACGTCTATGAAAATTCAAAACTCGACAGCGCTAACAGCAACAAAAACAGTCAA 89 −1.456082288 −1 Stayer TAAAGAAACGTCTATGAAAATTCAAAACTCGAGTTGAGTTTGATGTTAATTTCGTAAAAT 90 −1.48508913 −1 Stayer TAAAGAAACGTCTATGAAAATTCAAAACTCGATTCTGTAAAATGAAAAGCTTTTTCAGAG 91 −1.433306392 −1 Stayer TAAAGAAACGTCTATGAAAATTCAAAACTCGACAGTTATGTAAATCAAAGTATGAAGACA 92 −1.388999827 −1 Stayer TAAAGAAACGTCTATGAAAATTCAAAACTCGAGTCTTGAGTTTTAATGTAGATTAAGCCA 93 1.168920872 1 Sprinter CGGGCAAAAACTAGCTATTTAATATCTCTCGAGAGGGGCAGAATAAATGATCGCTAATGC 94 1.195108595 1 Sprinter GCATTAGCGATCATTTATTCTGCCCCTCTCGAAGACTCTGATGGTTTCTGGTTTGTTGAA 95 1.169269676 1 Sprinter GCATTAGCGATCATTTATTCTGCCCCTCTCGAGGTGGGGTTTTTCTTGCGCTTGCACTGT 96 1.184766624 1 Sprinter CTCCACTCATATGTGGAAATTAAACATGTCGATTCAGTTTTGATGGACGAGGTTCAGAGA 97 1.161449224 1 Sprinter TGTCTTCAATAAATTGTGTTGGGAAAATTCGAGTCCCTCCTACAACTCCACTTAATGGGG 98 1.332194988 1 Sprinter TGTCTTCAATAAATTGTGTTGGGAAAATTCGAAATGAGGGTTTCAATAGTTCAAAATTTT 99 1.325035367 1 Sprinter GAACGTGATGATGTAGTCTATACAGAAGTCGAAGTGAGACTTCTTCAAAAAAAGTTCACG 100 1.261850317 1 Sprinter GAACGTGATGATGTAGTCTATACAGAAGTCGAAGTTTCACACAATATTCTATTAACTCAC 101 1.204439572 1 Sprinter GAACGTGATGATGTAGTCTATACAGAAGTCGACTGAACACCACAATCCAACGGAAGTTCC 102 −1.14471456 −1 Stayer CAACGGCATGTTGGATGTACAAATGGGTTCGAATAGTTACCATCTGTAGTCTTGATCTCT 103 2.261606163 1 Sprinter AGAATTGGTAGGTATTGTAGTGATGTATTCGAAGATTGTTCATTATATCAAACCATGACA 104 1.147613384 1 Sprinter ACTGGAGACTAGGCAGAGGAAAAACCTTTCGAGACAATTTATGATCAGGAAAAATGGACC 105 −1.319743601 −1 Stayer AATATAGTACAGGAACATCTTAGATTCCTCGAGTTCACACAGCCAAGAATGATCCGATTT 106 −1.194082447 −1 Stayer GCTGCAGGAAGTGATGTCAAAAGGAGGGTCGAAAACTACCACATTTCCATTTCAGTTTAA 107 −1.146735237 −1 Stayer GCTGCAGGAAGTGATGTCAAAAGGAGGGTCGATCAGTGGTCAACCCTTGTAAGTTCATCA 108 −1.253365184 −1 Stayer TTCCTTCTCTGTACACAAAGAAGTGAACTCGACTGCATTAATTTTTCCTTTTGAAACAGT 109 −2.204998899 −1 Stayer GGGGCCAAGAGTAATGCTTCGTATATAGTCGAATTTCCACAAGTAATTTTGAATTTCAGG 110 −1.333991499 −1 Stayer GGTTAAGAGCAGAGCCTTTAAAATCAGATCGAGAGCCGCGAGTTATGAGCTCTCCGCCTT 111 −1.237312788 −1 Stayer AGAGTTTGGAGAAGGAAGTTGGTCTCCTTCGAGAGCCGCGAGTTATGAGCTCTCCGCCTT 112 −1.304753494 −1 Stayer ATGTATTTAAAAACATTTCTTGAAGGCCTCGAGAGCCGCGAGTTATGAGCTCTCCGCCTT 113 −1.290004103 −1 Stayer ACTTTTCATAGTTTCTCCTTCTAAACTCTCGAGAGCCGCGAGTTATGAGCTCTCCGCCTT 114 −1.336248961 −1 Stayer TTTAAGCTCTGAGTTAGTCTATTTTCTATCGAGAGCCGCGAGTTATGAGCTCTCCGCCTT 115 1.242082693 1 Sprinter AAAAGAAATTATAGAGTTAATTACCTCATCGATTTCTGTTTGGGATGTGACGTACAATTC 116 1.163503359 1 Sprinter TTGTATCATTAATTAGGGCTTTGAATGGTCGATTTCTGTTTGGGATGTGACGTACAATTC 117 −1.297821933 −1 Stayer TCATTCATGGGTGAGTTGGTACTTTTTCTCGATGCTCAAACAGTGTTTGCCAAGTGGATG 118 −1.271098804 −1 Stayer TCATTCATGGGTGAGTTGGTACTTTTTCTCGACCACCTGTATAGCTGTGAGGCCACTGGT 119 −1.146312385 −1 Stayer ATACCCACATTCTGACCCCCGAGTCAGCTCGACCACCTGTATAGCTGTGAGGCCACTGGT 120 1.177728649 1 Sprinter ACATCATTAGTCATTGTGGAAATACAAATCGAAGTGTTTTATTTTCAAGAGCAAAGGTTA 121 −1.247059943 −1 Stayer TGGGAGTACAGAGAAAATTCTATAAGATTCGAACATCCAGGGAATCCATATTTTCTTTTA 122 −1.482009871 −1 Stayer TTCCGTGACTCAGAGCTGTTGGTACCTTTCGAGTGCATTGAATGAGATGTAAGTCATCAC 123 −1.240570375 −1 Stayer TGGCCTCATAATTTTTCAATATGCTCAATCGATAATTTGCTGGAACAGCTCAGAGAACTC 124 1.20374878 1 Sprinter CACAATGAAAATTTGAAAATATTTTGAGTCGAAAACAAAATATTGGTTTCACCTAAGATA 125 −1.217978043 −1 Stayer CCGTTCACGGAAGAAGCGCAAGCCCTATTCGATCAGCTCTGGCGCCGTGGGGAGTGGAGC 126 1.328229112 1 Sprinter ATGAGAGACTCCCATTAAAAATCGTGTCTCGATGATTTACAGGAAGGCATCAACTAAAAA 127 1.210311644 1 Sprinter ATGAGAGACTCCCATTAAAAATCGTGTCTCGATGCAGAGCAGTGAATAATATGTGTGCAG 128 1.298388503 1 Sprinter ATGAGAGACTCCCATTAAAAATCGTGTCTCGACACCAAGAACTGAACATCTATACTCTTC

TABLE 33.b5 Probe Location 4 kb Sequence Location N Chr Start1 End1 Start2 End2 Chr Start1 End1 Start2 65 8 85390137 85390168 85431393 85431424 8 85390137 85394138 85431393 66 22 34961425 34961456 35009442 35009473 22 34957455 34961456 35005472 67 12 20785118 20785149 20922776 20922807 12 20785118 20789119 20918806 68 12 20843696 20843727 20922776 20922807 12 20843696 20847697 20918806 69 3 18959778 18959809 19074282 19074313 3 18955808 18959809 19070312 70 28 42579274 42579305 42607249 42607280 28 42579274 42583275 42607249 71 16 15151267 15151298 15203309 15203340 16 15147297 15151298 15199339 72 16 15151267 15151298 15264001 15264032 16 15147297 15151298 15260031 73 16 15151267 15151298 15255076 15255107 16 15147297 15151298 15255076 74 16 15151267 15151298 15301390 15301421 16 15147297 15151298 15301390 75 16 15151267 15151298 15332649 15332680 16 15147297 15151298 15328679 76 16 15165960 15165991 15239150 15239181 16 15165960 15169961 15235180 77 7 69179023 69179054 69225505 69225536 7 69179023 69183024 69221535 78 7 69225505 69225536 69328532 69328563 7 69221535 69225536 69328532 79 15 8888678 8888709 8973363 8973394 15 8884708 8888709 8973363 80 15 8888678 8888709 9032720 9032751 15 8884708 8888709 9028750 81 15 8936185 8936216 8973363 8973394 15 8936185 8940186 8973363 82 25 5777848 5777879 5838527 5838558 25 5777848 5781849 5838527 83 26 40666594 40666625 40680588 40680619 26 40666594 40670595 40680588 84 6 15299757 15299788 15377978 15378009 6 15299757 15303758 15374008 85 6 15443464 15443495 15487479 15487510 6 15439494 15443495 15487479 86 13 38904201 38904232 39195563 39195594 13 38904201 38908202 39191593 87 13 38931046 38931077 39195563 39195594 13 38931046 38935047 39191593 88 13 38974958 38974989 39195563 39195594 13 38974958 38978959 39191593 89 13 38981963 38981994 39195563 39195594 13 38981963 38985964 39191593 90 13 38999154 38999185 39195563 39195594 13 38999154 39003155 39191593 91 13 39073684 39073715 39195563 39195594 13 39073684 39077685 39191593 92 13 39112330 39112361 39195563 39195594 13 39112330 39116331 39191593 93 5 37768331 37768362 37808997 37809028 5 37768331 37772332 37805027 94 5 37768331 37768362 37803790 37803821 5 37768331 37772332 37803790 95 5 37768331 37768362 37834953 37834984 5 37768331 37772332 37834953 96 18 78530158 78530189 78600391 78600422 18 78526188 78530189 78600391 97 6 75012399 75012430 75092742 75092773 6 75012399 75016400 75092742 98 6 75012399 75012430 75098342 75098373 6 75012399 75016400 75098342 99 17 27888277 27888308 27983597 27983628 17 27888277 27892278 27983597 100 17 27888277 27888308 28023161 28023192 17 27888277 27892278 28023161 101 17 27888277 27888308 28087062 28087093 17 27888277 27892278 28087062 102 17 27991669 27991700 28044612 28044643 17 27987699 27991700 28040642 103 17 35244506 35244537 35523297 35523328 17 35244506 35248507 35523297 104 17 35555855 35555886 35584820 35584851 17 35551885 35555886 35584820 105 24 42597681 42597712 42656523 42656554 24 42593711 42597712 42652553 106 22 41633839 41633870 41882778 41882809 22 41633839 41637840 41878808 107 22 41845220 41845251 41882778 41882809 22 41845220 41849221 41878808 108 7 37223720 37223751 37244778 37244809 7 37223720 37227721 37244778 109 26 23335158 23335189 23360793 23360824 26 23335158 23339159 23360793 110 5 48256162 48256193 48407852 48407883 5 48252192 48256193 48407852 111 5 48248931 48248962 48407852 48407883 5 48248931 48252932 48407852 112 5 48265153 48265184 48407852 48407883 5 48261183 48265184 48407852 113 5 48306348 48306379 48407852 48407883 5 48302378 48306379 48407852 114 5 48370294 48370325 48407852 48407883 5 48370294 48374295 48407852 115 17 62037937 62037968 62292109 62292140 17 62033967 62037968 62292109 116 17 62167794 62167825 62292109 62292140 17 62163824 62167825 62292109 117 1 13016139 13016170 13161461 13161492 1 13012169 13016170 13161461 118 1 13016139 13016170 13213575 13213606 1 13012169 13016170 13209605 119 1 13139944 13139975 13213575 13213606 1 13135974 13139975 13209605 120 19 38827199 38827230 39055705 39055736 19 38827199 38831200 39055705 121 14 35404443 35404474 35458546 35458577 14 35404443 35408444 35458546 122 11 19330735 19330766 19434549 19434580 11 19330735 19334736 19434549 123 11 19378980 19379011 19494959 19494990 11 19375010 19379011 19490989 124 4 51008167 51008198 51111188 51111219 4 51008167 51012168 51107218 125 6 70794688 70794719 70820645 70820676 6 70794688 70798689 70816675 126 25 17093899 17093930 17175445 17175476 25 17089929 17093930 17171475 127 25 17093899 17093930 17167460 17167491 25 17089929 17093930 17167460 128 25 17093899 17093930 17209847 17209878 25 17089929 17093930 17205877

TABLE 33.b6 4 kb Sequence Location N End2 Probe Primer ID-1 65 85435394 CD226_8_85390137_85395670_85431393_85435046_RR OBD RD043.257 66 35009473 CD40_22_34955976_34961456_35003447_35009473_FF OBD RD043.261 67 20922807 CD5_12_20785118_20787274_20916990_20922807_RF OBD RD043.265 68 20922807 CD5_12_20843696_20847942_20916990_20922807_RF OBD RD043.269 69 19074313 CDH1_3_18955128_18959809_19065895_19074313_FF OBD RD043.273 70 42611250 CERK_28_42579274_42585201_42607249_42612447_RR OBD RD043.277 71 15203340 CHL1_16_15145284_15151298_15196227_15203340_FF OBD RD043.281 72 15264032 CHL1_16_15145284_15151298_15255076_15264032_FF OBD RD043.285 73 15259077 CHL1_16_15145284_15151298_15255076_15264032_FR OBD RD043.289 74 15305391 CHL1_16_15145284_15151298_15301390_15310795_FR OBD RD043.293 75 15332680 CHL1_16_15145284_15151298_15326701_15332680_FF OBD RD043.297 76 15239181 CHL1_16_15165960_15173124_15233430_15239181_RF OBD RD043.301 77 69225536 CHRDL2_7_69179023_69184961_69220436_69225536_RF OBD RD043.305 78 69332533 CHRDL2_7_69220436_69225536_69328532_69336827_FR OBD RD043.309 79 8977364 CHST10_15_8874159_8888709_8973363_8982576_FR OBD RD043.313 80 9032751 CHST10_15_8874159_8888709_9029805_9032751_FF OBD RD043.317 81 8977364 CHST10_15_8936185_8939355_8973363_8982576_RR OBD RD043.321 82 5842528 COL15A1_25_5777848_5781338_5838527_5844153_RR OBD RD043.325 83 40684589 COL18A1_26_40666594_40668538_40680588_40685271_RR OBD RD043.329 84 15378009 COL4A4_6_15299757_15310450_15375645_15378009_RF OBD RD043.333 85 15491480 COL4A4_6_15436171_15443495_15487479_15493934_FR OBD RD043.337 86 39195594 CREBBP_13_38904201_38905631_39179236_39195594_RF OBD RD043.341 87 39195594 CREBBP_13_38931046_38933583_39179236_39195594_RF OBD RD043.345 88 39195594 CREBBP_13_38974958_38977634_39179236_39195594_RF OBD RD043.349 89 39195594 CREBBP_13_38981963_38985123_39179236_39195594_RF OBD RD043.353 90 39195594 CREBBP_13_38999154_39003472_39179236_39195594_RF OBD RD043.357 91 39195594 CREBBP_13_39073684_39080240_39179236_39195594_RF OBD RD043.361 92 39195594 CREBBP_13_39112330_39113797_39179236_39195594_RF OBD RD043.365 93 37809028 CRP_5_37768331_37775673_37803790_37809028_RF OBD RD043.369 94 37807791 CRP_5_37768331_37775673_37803790_37809028_RR OBD RD043.373 95 37838954 CRP_5_37768331_37775673_37834953_37842330_RR OBD RD043.377 96 78604392 CTLA4_18_78522827_78530189_78600391_78604267_FR OBD RD043.381 97 75096743 DDIT3_6_75012399_75018811_75092742_75096887_RR OBD RD043.385 98 75102343 DDIT3_6_75012399_75018811_75098342_75106967_RR OBD RD043.389 99 27987598 DGKH_17_27888277_27893919_27983597_27991700_RR OBD RD043.393 100 28027162 DGKH_17_27888277_27893919_28023161_28030553_RR OBD RD043.397 101 28091063 DGKH_17_27888277_27893919_28087062_28095320_RR OBD RD043.401 102 28044643 DGKH_17_27983597_27991700_28038960_28044643_FF OBD RD043.405 103 35527298 DIAPH3_17_35244506_35247777_35523297_35543766_RR OBD RD043.409 104 35588821 DIAPH3_17_35550338_35555886_35584820_35594304_FR OBD RD043.413 105 42656554 DLK1_24_42596087_42597712_42651466_42656554_FF OBD RD043.417 106 41882809 DOK5_22_41633839_41639527_41876029_41882809_RF OBD RD043.421 107 41882809 DOK5_22_41845220_41849884_41876029_41882809_RF OBD RD043.425 108 37248779 ETS1_7_37223720_37228234_37244778_37252642_RR OBD RD043.429 109 23364794 GABPA_26_23335158_23338855_23360793_23370765_RR OBD RD043.433 110 48411853 GJA5_5_48248931_48256193_48407852_48413621_FR OBD RD043.437 111 48411853 GJA5_5_48248931_48256193_48407852_48413621_RR OBD RD043.441 112 48411853 GJA5_5_48256193_48265184_48407852_48413621_FR OBD RD043.445 113 48411853 GJA5_5_48297725_48306379_48407852_48413621_FR OBD RD043.449 114 48411853 GJA5_5_48370294_48376643_48407852_48413621_RR OBD RD043.453 115 62296110 GPC5_17_62030628_62037968_62292109_62298602_FR OBD RD043.457 116 62296110 GPC5_17_62161244_62167825_62292109_62298602_FR OBD RD043.461 117 13165462 GRK5_1_13009800_13016170_13161461_13167914_FR OBD RD043.465 118 13213606 GRK5_1_13009800_13016170_13204085_13213606_FF OBD RD043.469 119 13213606 GRK5_1_13135627_13139975_13204085_13213606_FF OBD RD043.473 120 39059706 GSK3B_19_38827199_38835574_39055705_39060019_RR OBD RD043.477 121 35462547 HDAC3_14_35404443_35406152_35458546_35471150_RR OBD RD043.481 122 19438550 HDAC5_11_19330735_19336727_19434549_19441692_RR OBD RD043.485 123 19494990 HDAC5_11_19372111_19379011_19491838_19494990_FF OBD RD043.489 124 51111219 HDAC9_4_51008167_51021720_51107519_51111219_RF OBD RD043.493 125 70820676 HOXC6_6_70794688_70801196_70818032_70820676_RF OBD RD043.497 126 17175476 HSDL2_25_17089584_17093930_17167460_17175476_FF OBD RD043.501 127 17171461 HSDL2_25_17089584_17093930_17167460_17175476_FR OBD RD043.505 128 17209878 HSDL2_25_17089584_17093930_17197980_17209878_FF OBD RD043.509

TABLE 33.b7 N Primer Sequence Primer ID-2 Primer Sequence 65 GTCAATGGAAGGAGGGAAATAATA OBD RD043.259 TCTCAACAGAGGAGTAAGATGTAT 66 CCTCGGACCTCTCTCGCTGATAC OBD RD043.263 GCCGTCAGTATTGTTTGGCTGGC 67 AGAACTGCTGGCAAGGGAGACAG OBD RD043.267 ACACAGAGAGAGCCCCTCAGAGC 68 AACTGCTGGCAAGGGAGACAGGG OBD RD043.271 GACAAGGGAAGGACCGAAAAGCC 69 AGCCTGAAGTGGGAACCAACCCC OBD RD043.275 GACAAGGTGGAAAGGTAGGCACG 70 ACTGTAAACCTGGGAACAACACCA OBD RD043.279 AATAAGTCCTCGGGATGTAATGTA 71 GGATGACCCTAACATTTCAGCAAACA OBD RD043.283 CCTACAATCACCACAGGACCTCTCCA 72 CTTTGCTCTTAGACCCTCCTTCCACA OBD RD043.287 GGATAGGAACAAAGCAAGAATGATGT 73 CTTTGCTCTTAGACCCTCCTTCCACA OBD RD043.291 GAAGATAGTGGAATGCTTTTGGTGAC 74 TGACCCTAACATTTCAGCAAACATTG OBD RD043.295 CACTAACAGAGCATTTTCTTCAAGGA 75 TGAAGGCAGGCTTTGTTCTATTTT OBD RD043.299 TGAAGAATAAAACCCAGACCAAAA 76 TTTGCTCTTAGACCCTCCTTCCACAT OBD RD043.303 GCCGACCTTCTGAGATACTAACGGTG 77 CTGTAGGTTCAACTTCTTATCAGTGC OBD RD043.307 CAGTTGTTAGCCCAGGTGCCAAT 78 CCCCTGTAGGTTCAACTTCTTATCAG OBD RD043.311 CCGTTTCCTACCAGTGTGACTACCAG 79 GTGAGCACAGAGTGAGAGAATCATCT OBD RD043.315 GCAGTCCCTATGAGAAACCCAGC 80 GTGAGCACAGAGTGAGAGAATCATCT OBD RD043.319 CAAATCTGGTGATAAATCCGCATCCA 81 AGGGAGGCTCACGCTGGCAGTAA OBD RD043.323 GCAGTCCCTATGAGAAACCCAGC 82 GTCAGCAACCATCATTATTTCCTA OBD RD043.327 TGTTACTCCGATACTGCTTTCTTA 83 GACTCCGCTGGCTCATCTCCTTC OBD RD043.331 GGACTTGCCCTCGGTGTTTTGTG 84 GGCATACTGTCGTGTCTCAGGAG OBD RD043.335 CCTCCTCTCCCTTCTGCCATCAG 85 CACTCGTGGCATTGAAACCAAAGTCT OBD RD043.339 AGTCTGTCTTCACTAACGATGGC 86 CTGACCTGCTCCCCAGTGAAACT OBD RD043.343 TCCCTTTTCCTGCCTCCCTCCCC 87 CTGACCTGCTCCCCAGTGAAACT OBD RD043.347 GACAGTGGTCTCCTTCTTACCTG 88 CTGACCTGCTCCCCAGTGAAACT OBD RD043.351 CAGGGACAATCACTTCTAAACACTAA 89 CTGACCTGCTCCCCAGTGAAACT OBD RD043.355 GTTTTGTTGACTTCTCACCAGCAAGA 90 CTGACCTGCTCCCCAGTGAAACT OBD RD043.359 ATCCACACAGAAGTTAGGGCTGC 91 ATGCTGACCTGCTCCCCAGTGAA OBD RD043.363 AGGAAGAGCAGCACCAGGCACCT 92 CTGACCTGCTCCCCAGTGAAACT OBD RD043.367 CCACATTTCTCACTTCAGGTAAGC 93 GGAGAAAGCAACCAATGAACGGAAGA OBD RD043.371 GATTTCCCTCTGTCCTGCCTCAATGC 94 TTCCCTCTGTCCTGCCTCAATGC OBD RD043.375 CAAGCGGAGAGAGACGACACTGC 95 GTGCGGTCACAAGAATCTCTAATACG OBD RD043.379 CTTTCCGCACCCTCTGAACTTTTGGG 96 GTGAAATAAGCCAGATAGAGAAAGAC OBD RD043.383 GAGCGAAAGAACGGATGAAGCATTTT 97 TAGAGAGCCCAGAAATAAATCCAT OBD RD043.387 CAGGACCATCAAGATAAATGAATA 98 GAATAGAGAGCCCAGAAATAAATCCA OBD RD043.391 TGGAGGAAGGGAGCCAGGACCCC 99 GCGACACCTCCTCTGTTGCCAAG OBD RD043.395 GCACCACTGGCAGAGTTTACGGT 100 TACAGAGAACAGATTGGTGGTCAC OBD RD043.399 CTGGAGAAAAGGAGTATGGAGAAT 101 TACAGAGAACAGATTGGTGGTCAC OBD RD043.403 AAGGCTTTTATGTGAACAGAGATA 102 TACAGAGAACAGATTGGTGGTCAC OBD RD043.407 GAAATAAAGTCAATCTTCCTGAAAA 103 CACTGCCACAAAAGCCGCTCTGG OBD RD043.411 CACTGACTACACGGAAGATGGCG 104 GAAAGATGCCCAGTCTGTGTCGGAGA OBD RD043.415 TTTTGACCAGCAGATAGTGTCGTGTC 105 TGGAGTAAGACGCCGAAAACACT OBD RD043.419 GGGCACTCTGGATTGAGACAGTA 106 AGGAGTCCCTGCCCTCGGAATCT OBD RD043.423 GCTTCCCAGAACCCAAATCTCCC 107 AGGAGTCCCTGCCCTCGGAATCT OBD RD043.427 CTTCCGATGGACGAATCTCAGGC 108 GCAGGGAGTCAGTCATTTTGTTTCTC OBD RD043.431 CCCTCCAATGAAAGTAGTCTGCCTGC 109 TTATCTTCTTTACCTACATTCCAGGG OBD RD043.435 TGGGCACAAAGGGTGAAGTGGTG 110 ACTTACAAACCCAATCACTACATA OBD RD043.439 GGAAGACCAGAGAACAGAACTGAT 111 AATCTATTCCCACTCACCTCTGG OBD RD043.443 GGAAGACCAGAGAACAGAACTGAT 112 GAATAGGTCCTTTTGTTTTGTTTT OBD RD043.447 GGAAGACCAGAGAACAGAACTGAT 113 ACGGAAGCAGAATGGAGAGTGGG OBD RD043.451 GGAAGACCAGAGAACAGAACTGAT 114 CCCAAGTGCTGCTTCTATTTCCT OBD RD043.455 GGAAGACCAGAGAACAGAACTGAT 115 TCCCAGATTCTACCCTTGACCCTCAT OBD RD043.459 GACCTCAACAGAAAGTCCTCAACAGG 116 GGATGAGTTCTAAATGAATAATGA OBD RD043.463 CCTCAACAGAAAGTCCTCAACAGG 117 ATTGAGTGGCTGGCGGTCACGGT OBD RD043.467 GGTCCTGCTCTATCTTTCCCCTC 118 TTATTGAGTGGCTGGCGGTCACG OBD RD043.471 AGGGCTTCAGCAGGCAGAGGGAT 119 GGTGGCAAAAGCCCCAAGAGAATGAG OBD RD043.475 GGTAACTTGAAATAAGCCACAGAGGG 120 GGCAAAGGACTTGAAAAGACATTT OBD RD043.479 TTGAAGTTTACCAGGAGAGGAAAA 121 GAGGATTGGCAGCAGATGTTAGC OBD RD043.483 GGAGATGAAAGACAATGGATGAGATA 122 CCCTACCAGGCTCAGATGGGATT OBD RD043.487 CCTGCCTCCCCTCACAACACACA 123 CCCAGGACCCAGGTTTTCTTACC OBD RD043.491 CTCGCCCTGTGTAGCACCTCTCT 124 TGTGCCCATCTTCCTCTACTTTAT OBD RD043.495 TCCAACATTGCTTTACTCTTATGA 125 CCCTACTGGTTCATCTCCACCCA OBD RD043.499 GCCGCTTCCACCCAGGACAGTAA 126 CCCCTCTCCAGCAGTTTTGAGTAATA OBD RD043.503 CTGACACTGAGCACAGGGTTTGGAAG 127 GCCCCTCTCCAGCAGTTTTGAGTAAT OBD RD043.507 GAGAGAAGCCACCAAGATAAGTCCAC 128 CCCTCTCCAGCAGTTTTGAGTAA OBD RD043.511 CTTTGTTTACCTGGCATCTTGAGTCA

TABLE 33.b8 N Probe Marker 65 CD226 OBD RD043.257.259 66 CD40 OBD RD043.261.263 67 CD5 OBD RD043.265.267 68 CD5 OBD RD043.269.271 69 CDH1 OBD RD043.273.275 70 CERK OBD RD043.277.279 71 CHL1 OBD RD043.281.283 72 CHL1 OBD RD043.285.287 73 CHL1 OBD RD043.289.291 74 CHL1 OBD RD043.293.295 75 CHL1 OBD RD043.297.299 76 CHL1 OBD RD043.301.303 77 CHRDL2 OBD RD043.305.307 78 CHRDL2 OBD RD043.309.311 79 CHST10 OBD RD043.313.315 80 CHST10 OBD RD043.317.319 81 CHST10 OBD RD043.321.323 82 COL15A1 OBD RD043.325.327 83 COL18A1 OBD RD043.329.331 84 COL4A4 OBD RD043.333.335 85 COL4A4 OBD RD043.337.339 86 CREBBP OBD RD043.341.343 87 CREBBP OBD RD043.345.347 88 CREBBP OBD RD043.349.351 89 CREBBP OBD RD043.353.355 90 CREBBP OBD RD043.357.359 91 CREBBP OBD RD043.361.363 92 CREBBP OBD RD043.365.367 93 CRP OBD RD043.369.371 94 CRP OBD RD043.373.375 95 CRP OBD RD043.377.379 96 CTLA4 OBD RD043.381.383 97 DDIT3 OBD RD043.385.387 98 DDIT3 OBD RD043.389.391 99 DGKH OBD RD043.393.395 100 DGKH OBD RD043.397.399 101 DGKH OBD RD043.401.403 102 DGKH OBD RD043.405.407 103 DIAPH3 OBD RD043.409.411 104 DIAPH3 OBD RD043.413.415 105 DLK1 OBD RD043.417.419 106 DOK5 OBD RD043.421.423 107 DOK5 OBD RD043.425.427 108 ETS1 OBD RD043.429.431 109 GABPA OBD RD043.433.435 110 GJA5 OBD RD043.437.439 111 GJA5 OBD RD043.441.443 112 GJA5 OBD RD043.445.447 113 GJA5 OBD RD043.449.451 114 GJA5 OBD RD043.453.455 115 GPC5 OBD RD043.457.459 116 GPC5 OBD RD043.461.463 117 GRK5 OBD RD043.465.467 118 GRK5 OBD RD043.469.471 119 GRK5 OBD RD043.473.475 120 GSK3B OBD RD043.477.479 121 HDAC3 OBD RD043.481.483 122 HDAC5 OBD RD043.485.487 123 HDAC5 OBD RD043.489.491 124 HDAC9 OBD RD043.493.495 125 HOXC6 OBD RD043.497.499 126 HSDL2 OBD RD043.501.503 127 HSDL2 OBD RD043.505.507 128 HSDL2 OBD RD043.509.511

TABLE 33.c1 N Probe GeneLocus Probe_Count_Total Probe_Count_Sig 129 IGF1_28_26127450_26135782_26165074_26175137_FF IGF1 1 83 130 IL17F_20_49908438_49915179_49992351_49998114_RR IL17F 1 23 131 IL1R1_15_7480700_7491275_7547275_7554471_FR IL1R1 1 34 132 IL1RAP_19_27981648_27987302_28153765_28161424_FR IL1RAP 3 212 133 IL1RAP_19_28069654_28081538_28153765_28161424_FR IL1RAP 3 212 134 IL1RAP_19_28153765_28161424_28173183_28182762_RR IL1RAP 3 212 135 IL21R_13_20649899_20654880_20738447_20749797_FF IL21R 1 43 136 IL6ST_21_16316515_16320787_16507936_16519953_RF IL6ST 5 74 137 IL6ST_21_16361905_16367133_16507936_16519953_RF IL6ST 5 74 138 IL6ST_21_16380568_16382969_16507936_16519953_FF IL6ST 5 74 139 IL6ST_21_16389402_16396020_16507936_16519953_RF IL6ST 5 74 140 IL6ST_21_16427757_16430421_16507936_16519953_FF IL6ST 5 74 141 IPMK_1_47907514_47915619_47934069_47940539_RF IPMK 1 49 142 KCND3_5_56337143_56347199_56370847_56374140_RF KCND3 2 315 143 KCND3_5_56337143_56347199_56514669_56519275_RF KCND3 2 315 144 KCNE2_26_30910971_30912196_30981829_30991799_FF KCNE2 2 53 145 KCNE2_26_30910971_30912196_30981829_30991799_FR KCNE2 2 53 146 KCNH2_4_102471847_102478321_102526070_102533652_RF KCNH2 1 31 147 KCNJ2_11_10875120_10880378_10941535_10945829_RF KCNJ2 2 24 148 KCNJ2_11_10907501_10914338_10941535_10945829_RF KCNJ2 2 24 149 KDM1A_2_31709535_31721093_31731426_31738065_RR KDM1A 8 105 150 KDM1A_2_31709535_31721093_31749361_31751529_RR KDM1A 8 105 151 KDM1A_2_31709535_31721093_31757482_31759922_RR KDM1A 8 105 152 KDM1A_2_31709535_31721093_31759922_31772142_RR KDM1A 8 105 153 KDM1A_2_31709535_31721093_31779719_31783168_RR KDM1A 8 105 154 KDM1A_2_31709535_31721093_31795486_31798526_RR KDM1A 8 105 155 KDM1A_2_31709535_31721093_31816722_31820715_RR KDM1A 8 105 156 KDM1A_2_31709535_31721093_31841824_31843977_RR KDM1A 8 105 157 LAMA2_10_75419882_75421720_75481925_75491582_FF LAMA2 33 325 158 LAMA2_10_75419882_75421720_75481925_75491582_FR LAMA2 33 325 159 LAMA2_10_75419882_75421720_75481925_75491582_RR LAMA2 33 325 160 LAMA2_10_75433825_75441819_75481925_75491582_RR LAMA2 33 325 161 LAMA2_10_75481925_75491582_75503397_75505438_RF LAMA2 33 325 162 LAMA2_10_75481925_75491582_75503397_75505438_RR LAMA2 33 325 163 LAMA2_10_75481925_75491582_75510267_75513025_RR LAMA2 33 325 164 LAMA2_10_75481925_75491582_75515462_75518504_RF LAMA2 33 325 165 LAMA2_10_75481925_75491582_75515462_75518504_RR LAMA2 33 325 166 LAMA2_10_75481925_75491582_75537867_75543336_RR LAMA2 33 325 167 LAMA2_10_75481925_75491582_75558780_75560310_RR LAMA2 33 325 168 LAMA2_10_75481925_75491582_75583879_75585705_RF LAMA2 33 325 169 LAMA2_10_75481925_75491582_75583879_75585705_RR LAMA2 33 325 170 LAMA2_10_75481925_75491582_75598703_75603065_RR LAMA2 33 325 171 LAMA2_10_75481925_75491582_75630159_75632019_RR LAMA2 33 325 172 LAMA2_10_75481925_75491582_75657275_75659989_RF LAMA2 33 325 173 LAMA2_10_75481925_75491582_75657275_75659989_RR LAMA2 33 325 174 LAMA2_10_75481925_75491582_75673465_75680786_RF LAMA2 33 325 175 LAMA2_10_75481925_75491582_75673465_75680786_RR LAMA2 33 325 176 LAMA2_10_75481925_75491582_75689296_75698651_RF LAMA2 33 325 177 LAMA2_10_75481925_75491582_75689296_75698651_RR LAMA2 33 325 178 LAMA2_10_75481925_75491582_75699217_75700676_RR LAMA2 33 325 179 LAMA2_10_75481925_75491582_75710114_75711790_RF LAMA2 33 325 180 LAMA2_10_75481925_75491582_75710114_75711790_RR LAMA2 33 325 181 LAMA2_10_75481925_75491582_75727142_75730779_RR LAMA2 33 325 182 LAMA2_10_75481925_75491582_75731193_75737098_RF LAMA2 33 325 183 LAMA2_10_75481925_75491582_75731193_75737098_RR LAMA2 33 325 184 LAMA2_10_75481925_75491582_75761081_75765848_RR LAMA2 33 325 185 LAMA2_10_75481925_75491582_75767487_75769615_RF LAMA2 33 325 186 LAMA2_10_75481925_75491582_75772669_75776905_RR LAMA2 33 325 187 LAMA2_10_75481925_75491582_75789669_75791964_RF LAMA2 33 325 188 LAMA2_10_75985731_76002512_76077151_76079817_FF LAMA2 33 325 189 LAMA2_10_75985731_76002512_76077151_76079817_RF LAMA2 33 325 190 LDB2_3_106480842_106484500_106716847_106728445_RR LDB2 2 196 191 LDB2_3_106716847_106728445_106944178_106947885_RF LDB2 2 196 192 LEPR_5_95193431_95200537_95211956_95218723_RR LEPR 1 31

TABLE 33.c2 N HyperG_Stats FDR_HyperG 129 0.346998557 0.36994061 130 0.157480479 0.267074007 131 0.212678487 0.282840462 132 0.154850013 0.267074007 133 0.154850013 0.267074007 134 0.154850013 0.267074007 135 0.249797286 0.310300562 136 0.00033129 0.004748485 137 0.00033129 0.004748485 138 0.00033129 0.004748485 139 0.00033129 0.004748485 140 0.00033129 0.004748485 141 0.270953196 0.310300562 142 0.253289491 0.310300562 143 0.253289491 0.310300562 144 0.060873696 0.137915817 145 0.060873696 0.137915817 146 0.198752749 0.267074007 147 0.015462469 0.066488616 148 0.015462469 0.066488616 149 0.00000240079898941557 0.000103234 150 0.00000240079898941557 0.000103234 151 0.00000240079898941557 0.000103234 152 0.00000240079898941557 0.000103234 153 0.00000240079898941557 0.000103234 154 0.00000240079898941557 0.000103234 155 0.00000240079898941557 0.000103234 156 0.00000240079898941557 0.000103234 157 0.0000000000000000000000000509616413350981 0.00000000000000000000000657405173222766 158 0.0000000000000000000000000509616413350981 0.00000000000000000000000657405173222766 159 0.0000000000000000000000000509616413350981 0.00000000000000000000000657405173222766 160 0.0000000000000000000000000509616413350981 0.00000000000000000000000657405173222766 161 0.0000000000000000000000000509616413350981 0.00000000000000000000000657405173222766 162 0.0000000000000000000000000509616413350981 0.00000000000000000000000657405173222766 163 0.0000000000000000000000000509616413350981 0.00000000000000000000000657405173222766 164 0.0000000000000000000000000509616413350981 0.00000000000000000000000657405173222766 165 0.0000000000000000000000000509616413350981 0.00000000000000000000000657405173222766 166 0.0000000000000000000000000509616413350981 0.00000000000000000000000657405173222766 167 0.0000000000000000000000000509616413350981 0.00000000000000000000000657405173222766 168 0.0000000000000000000000000509616413350981 0.00000000000000000000000657405173222766 169 0.0000000000000000000000000509616413350981 0.00000000000000000000000657405173222766 170 0.0000000000000000000000000509616413350981 0.00000000000000000000000657405173222766 171 0.0000000000000000000000000509616413350981 0.00000000000000000000000657405173222766 172 0.0000000000000000000000000509616413350981 0.00000000000000000000000657405173222766 173 0.0000000000000000000000000509616413350981 0.00000000000000000000000657405173222766 174 0.0000000000000000000000000509616413350981 0.00000000000000000000000657405173222766 175 0.0000000000000000000000000509616413350981 0.00000000000000000000000657405173222766 176 0.0000000000000000000000000509616413350981 0.00000000000000000000000657405173222766 177 0.0000000000000000000000000509616413350981 0.00000000000000000000000657405173222766 178 0.0000000000000000000000000509616413350981 0.00000000000000000000000657405173222766 179 0.0000000000000000000000000509616413350981 0.00000000000000000000000657405173222766 180 0.0000000000000000000000000509616413350981 0.00000000000000000000000657405173222766 181 0.0000000000000000000000000509616413350981 0.00000000000000000000000657405173222766 182 0.0000000000000000000000000509616413350981 0.00000000000000000000000657405173222766 183 0.0000000000000000000000000509616413350981 0.00000000000000000000000657405173222766 184 0.0000000000000000000000000509616413350981 0.00000000000000000000000657405173222766 185 0.0000000000000000000000000509616413350981 0.00000000000000000000000657405173222766 186 0.0000000000000000000000000509616413350981 0.00000000000000000000000657405173222766 187 0.0000000000000000000000000509616413350981 0.00000000000000000000000657405173222766 188 0.0000000000000000000000000509616413350981 0.00000000000000000000000657405173222766 189 0.0000000000000000000000000509616413350981 0.00000000000000000000000657405173222766 190 0.260903936 0.310300562 191 0.260903936 0.310300562 192 0.198752749 0.267074007

TABLE 33.c3 N Percent_Sig logFC AveExpr t P.Value 129 1.2 −0.25974584 9.184771261 −5.05789465 0.0000686965968072954 130 4.35 −0.42286988 9.795885578 −8.986284737 0.0000000272316278242442 131 2.94 −0.285238748 8.475210157 −5.003309015 0.0000776210585910804 132 1.42 −0.233297428 7.917147257 −5.063868868 0.0000677854972204880 133 1.42 −0.261678217 7.906642716 −7.35841864 0.000000547113238929680 134 1.42 −0.247346127 10.12235567 −6.078434637 0.00000741791913423433 135 2.33 −0.504771054 9.843131031 −10.25775021 0.00000000328750499948560 136 6.76 −0.416415403 12.34496702 −5.613648976 0.0000201456451707163 137 6.76 −0.426151333 12.51889676 −5.249917488 0.0000448018862245979 138 6.76 −0.23353917 12.44377995 −5.538440914 0.0000237375958014509 139 6.76 −0.411700512 12.62002559 −5.185430873 0.0000516971247274845 140 6.76 −0.223557802 11.04467508 −5.194995118 0.0000506097781533960 141 2.04 0.248972748 9.763034476 5.472372277 0.0000274322269039290 142 0.63 −0.826874049 9.755934263 −11.64073761 0.000000000403131843228993 143 0.63 −0.188752779 9.124965652 −5.134174071 0.0000579439468653047 144 3.77 −0.263863415 9.389840285 −5.665269959 0.0000180067783076360 145 3.77 −0.277105906 9.211949107 −5.081146529 0.0000652192037780800 146 3.23 −0.350022028 11.18568763 −6.168156484 0.00000613563582584375 147 8.33 0.694351653 8.391007916 7.96791572 0.000000170820887322144 148 8.33 0.461719332 8.783986871 6.236727656 0.00000531090520632885 149 7.62 −0.734667206 8.882775953 −7.565318365 0.000000366473080287362 150 7.62 −0.260872283 10.51288503 −6.881875363 0.00000140759853742685 151 7.62 −0.302726916 10.11606951 −5.433872607 0.0000298515328569823 152 7.62 −0.53472543 9.308125792 −11.46362698 0.000000000521792977583466 153 7.62 −0.364206415 9.729541969 −6.308264284 0.00000457138115916845 154 7.62 −0.460314357 9.475119298 −7.40716807 0.000000497560114213970 155 7.62 −0.621721431 8.876491488 −7.539008509 0.000000385508372459963 156 7.62 −0.47363865 9.446359898 −7.234458458 0.000000697508104712342 157 10.15 −0.501711845 10.09895493 −8.589317091 0.0000000548373634182702 158 10.15 −0.428220161 13.02189528 −7.167747421 0.000000795580379158680 159 10.15 −0.339941253 12.88803216 −5.561186413 0.0000225869301073419 160 10.15 −0.228417033 13.56928534 −5.920840322 0.0000103781975494252 161 10.15 −0.30207162 13.37620496 −5.439499489 0.0000294847593610427 162 10.15 −0.39204058 13.89495223 −5.801140554 0.0000134209610425670 163 10.15 −0.343069197 13.96715152 −6.417777669 0.00000363844975130824 164 10.15 −0.354475767 13.22017743 −5.259160113 0.0000438935269293937 165 10.15 −0.446958091 13.8037429 −5.840868856 0.0000123208089585518 166 10.15 −0.379960986 13.89492979 −6.236715524 0.00000531104056573792 167 10.15 −0.449915255 13.94340659 −9.137780656 0.0000000209555895296964 168 10.15 −0.356701022 12.87002792 −5.553163982 0.0000229861111463834 169 10.15 −0.428629599 13.82169896 −6.617643858 0.00000240861706096913 170 10.15 −0.419629634 13.93664391 −8.158999079 0.000000119804038144258 171 10.15 −0.430573855 13.96364886 −8.446068963 0.0000000709422502038841 172 10.15 −0.256004051 13.24896441 −5.56584902 0.0000223581954829190 173 10.15 −0.41467922 14.1640228 −7.07939174 0.000000947891998878803 174 10.15 −0.331716046 12.41203838 −4.98917938 0.0000801177911327344 175 10.15 −0.393636052 13.86311599 −5.696573254 0.0000168245001760445 176 10.15 −0.33697792 12.45047432 −5.039670375 0.0000715536819400699 177 10.15 −0.43042349 13.94505376 −5.895952776 0.0000109465097531085 178 10.15 −0.417317056 13.83868121 −7.743329932 0.000000260799615293896 179 10.15 −0.349687395 12.88984807 −6.592764316 0.00000253479528084738 180 10.15 −0.401014761 13.96210217 −5.511317857 0.0000251885049881526 181 10.15 −0.376700577 13.82296798 −7.462445086 0.000000446952562820082 182 10.15 −0.361735429 12.82385418 −5.647753484 0.0000187051686375902 183 10.15 −0.384425532 13.87283328 −5.612599396 0.0000201917366403219 184 10.15 −0.481052786 13.9255892 −9.4062159 0.0000000132641985345548 185 10.15 −0.302151184 13.18318606 −5.156392006 0.0000551467689003870 186 10.15 −0.362843331 14.28924283 −6.234521481 0.00000533557766392404 187 10.15 −0.346934118 12.83387771 −5.572053104 0.0000220575120754949 188 10.15 −0.387765562 8.971457443 −8.562458613 0.0000000575383157451633 189 10.15 −0.346223991 10.11461327 −6.659629102 0.00000221017993365992 190 1.02 −0.479413897 9.999705501 −7.255881323 0.000000668739609939400 191 1.02 −0.24620165 9.243513309 −5.088361737 0.0000641770071013719 192 3.23 0.414997972 6.542688969 7.586596983 0.000000351791539018826

TABLE 33.c4 N adj.P.Val B FC FC_1 LS Loop Detected 129 0.00881531 1.792843727 0.83523505 −1.197267763 −1 Stayer 130 0.000048275438684640 9.106256241 0.745939288 −1.340591675 −1 Stayer 131 0.00961269 1.676496246 0.820605797 −1.218611912 −1 Stayer 132 0.008756001 1.805561135 0.850688333 −1.17551865 −1 Stayer 133 0.00033823 6.355209789 0.834117067 −1.198872484 −1 Stayer 134 0.002009535 3.907359412 0.842444688 −1.18702155 −1 Stayer 135 0.00000854970466866222 10.98597877 0.704772211 −1.418898169 −1 Stayer 136 0.0039679 2.96000383 0.749284025 −1.334607395 −1 Stayer 137 0.006607886 2.199880493 0.744244555 −1.343644361 −1 Stayer 138 0.004367942 2.804099038 0.8505458 −1.17571564 −1 Stayer 139 0.007221168 2.063594435 0.751736775 −1.330252866 −1 Stayer 140 0.007179227 2.083834368 0.856450753 −1.167609458 −1 Stayer 141 0.004693558 2.666578884 1.188360657 1.188360657 1 Sprinter 142 0.00000262102886739384 12.79107546 0.563749421 −1.773837743 −1 Stayer 143 0.007875935 1.954968861 0.877363882 −1.139777943 −1 Stayer 144 0.003741337 3.066609893 0.832854617 −1.200689748 −1 Stayer 145 0.008590182 1.842321715 0.825244826 −1.211761611 −1 Stayer 146 0.001721951 4.086856496 0.784572118 −1.274580088 −1 Stayer 147 0.00016253 7.432545616 1.61815707 1.61815707 1 Sprinter 148 0.001576825 4.223269904 1.377182098 1.377182098 1 Sprinter 149 0.000274925 6.727366085 0.600956635 −1.664013578 −1 Stayer 150 0.000606823 5.472840867 0.834583161 −1.198202944 −1 Stayer 151 0.004995541 2.58620654 0.810718564 −1.233473667 −1 Stayer 152 0.00000265148685080001 12.57279103 0.690290038 −1.448666422 −1 Stayer 153 0.001426637 4.364862947 0.776896105 −1.287173398 −1 Stayer 154 0.00032898 6.443494308 0.726827869 −1.375841575 −1 Stayer 155 0.000283749 6.680410031 0.649895007 −1.538710083 −1 Stayer 156 0.000406116 6.129060869 0.720146011 −1.388607289 −1 Stayer 157 0.000076400198105240 8.472295113 0.706268254 −1.415892608 −1 Stayer 158 0.000449791 6.006370737 0.743178071 −1.345572533 −1 Stayer 159 0.004245102 2.851322566 0.790073483 −1.265705053 −1 Stayer 160 0.002530334 3.5893669 0.853570941 −1.171548787 −1 Stayer 161 0.004957761 2.597963987 0.81108689 −1.23291353 −1 Stayer 162 0.003061706 3.345590015 0.76205098 −1.312248165 −1 Stayer 163 0.001213128 4.580182501 0.788362361 −1.268452237 −1 Stayer 164 0.006535445 2.219378577 0.782153803 −1.27852092 −1 Stayer 165 0.002843993 3.426710531 0.733587982 −1.363163008 −1 Stayer 166 0.001576825 4.223245828 0.768458371 −1.301306665 −1 Stayer 167 0.000038927502264450 9.342123058 0.73208585 −1.365960017 −1 Stayer 168 0.004269944 2.834673761 0.780948316 −1.28049447 −1 Stayer 169 0.000894859 4.968583134 0.742967187 −1.345954461 −1 Stayer 170 0.000119835 7.758516636 0.747616527 −1.337584128 −1 Stayer 171 0.000081395799425103 8.23778519 0.741966597 −1.347769567 −1 Stayer 172 0.004245102 2.860995205 0.837404136 −1.19416654 −1 Stayer 173 0.000513573 5.842814484 0.750186279 −1.333002254 −1 Stayer 174 0.009828286 1.64633615 0.794590778 −1.258509447 −1 Stayer 175 0.00361547 3.131093689 0.761208696 −1.313700179 −1 Stayer 176 0.009092212 1.754029209 0.791697982 −1.26310793 −1 Stayer 177 0.002605462 3.538839183 0.742043933 −1.347629103 −1 Stayer 178 0.0002366 7.042253477 0.748815885 −1.335441756 −1 Stayer 179 0.000932852 4.920559418 0.784754121 −1.274284484 −1 Stayer 180 0.00443021 2.747705761 0.757325409 −1.320436351 −1 Stayer 181 0.000311021 6.543154484 0.770197007 −1.298369106 −1 Stayer 182 0.003840466 3.030472673 0.77822788 −1.284970669 −1 Stayer 183 0.0039679 2.957832836 0.766083985 −1.305339909 −1 Stayer 184 0.000025871819241649 9.751972552 0.716454611 −1.395761832 −1 Stayer 185 0.007628636 2.002085961 0.81104216 −1.232981526 −1 Stayer 186 0.001576825 4.21889148 0.777630478 −1.285957827 −1 Stayer 187 0.004238737 2.873861568 0.786253196 −1.271854925 −1 Stayer 188 0.000077398955076511 8.4285593 0.764312451 −1.308365444 −1 Stayer 189 0.000837079 5.049414099 0.786640303 −1.271229043 −1 Stayer 190 0.000395266 6.168314166 0.717268959 −1.394177159 −1 Stayer 191 0.008515459 1.857664798 0.843113258 −1.18608027 −1 Stayer 192 0.000270685 6.765264284 1.333296803 1.333296803 1 Sprinter

TABLE 33.c5 Probe sequence Probe Location N 60 mer Chr Start1 129 TTCCTTCATCATTTGTTATTTCCTCTGTTCGAATAGGGCTGAACCAATGGCCATACACAC 28 26135751 130 GAGGCCCATTGCAGGTACTTGGGCTGCATCGATTATCCCACTACACAGGATTTATATAAG 20 49908438 131 CCAGACTGAATTTTGTACAGAGTACACCTCGAAGTAATCTGACTTTAAAATGGTTCTTTT 15 7491244 132 TGGTAAGTGTATTATATAAGAAAAAAACTCGATCCTCTAATCCTGAATACCAGGTTGGGC 19 27987271 133 TTGCATTCATTCTTTTGCAGAAACATACTCGATCCTCTAATCCTGAATACCAGGTTGGGC 19 28081507 134 GCCCAACCTGGTATTCAGGATTAGAGGATCGAGAAGCCAGGCATGAATTCTGGTGTTTGC 19 28153765 135 CTCGTCAGTACTCTCAGTGTTTCCTCATTCGATCACTTTGGACATTTTAACAGCACTAAG 13 20654849 136 TCTTGCCCGAAGGCAGAGAGCTCAGAACTCGAAGTGAGCAGGATTTATTGAATAACAGAA 21 16316515 137 TCTTGCCCGAAGGCAGAGAGCTCAGAACTCGAACACTCTTGTTCTGCTTCCTCATCACTT 21 16361905 138 TTGCTTGGGTTTATGATTTTGTGCGGGGTCGAGTTCTGAGCTCTCTGCCTTCGGGCAAGA 21 16382938 139 TCTTGCCCGAAGGCAGAGAGCTCAGAACTCGAGCTGCTGCAGTCATTTTGTCACCATACA 21 16389402 140 CTGTCTAGTATCTTAAAATTGACATGGATCGAGTTCTGAGCTCTCTGCCTTCGGGCAAGA 21 16430390 141 AGTCTATCCAATTACAGTAATTTAAGCTTCGAGAGCCTGTGGTCTAAGAAAGAGTGAGAG 1 47907514 142 CCTTAGTACCTGCTTAGTACCCGCTTTGTCGAAGCAAAAGCAATTACCACCCCCAGCTTT 5 56337143 143 TAAAAACACATTTACAGTGCCACTGTACTCGAAGCAAAAGCAATTACCACCCCCAGCTTT 5 56337143 144 GACCTCCCTTACAGTACCTGCAGACTTGTCGATGAACTCCCACTCCAGTGGTGAGAAACC 26 30912165 145 GACCTCCCTTACAGTACCTGCAGACTTGTCGAGTTCCCATATGGGCAGTATGTAGGGCAC 26 30912165 146 TAATTCTCTGTAGTGAATCCCTTCCTGATCGAGGGGGCATCACAGAGTCAAAGGCAGCGA 4 102471847 147 GGAATATAATCTAACACCGTGTAACCATTCGACTCCAAATAAACTGAATACAGAAAGTTT 11 10875120 148 GGAATATAATCTAACACCGTGTAACCATTCGAAAATTTTGAAACAATTCCTCTGCCATTT 11 10907501 149 GGTACTAGATGACGTAGTCCGATAAGATTCGATTTCCCCATCTGTAAAATGTTTTCTTTG 2 31709535 150 GGTACTAGATGACGTAGTCCGATAAGATTCGACACAAATCCCCCTGCTACTGTTTAATTC 2 31709535 151 GGTACTAGATGACGTAGTCCGATAAGATTCGAAAAGTTCTGCCAGTCCTCCACTTACAGC 2 31709535 152 GGTACTAGATGACGTAGTCCGATAAGATTCGAAACCCGAAATAAAATTCTTACCCTGGCT 2 31709535 153 GGTACTAGATGACGTAGTCCGATAAGATTCGAGTTCCAATTCCTTAGCCTGGTAACCAAG 2 31709535 154 GGTACTAGATGACGTAGTCCGATAAGATTCGACAACATTCTGGTGTGACTGTGAATGAGC 2 31709535 155 GGTACTAGATGACGTAGTCCGATAAGATTCGACTCTGCAGAGTTCTCACTACTCCGCTTG 2 31709535 156 GGTACTAGATGACGTAGTCCGATAAGATTCGATTGGTTTGGCTGTTCTTGATCCGTTTAC 2 31709535 157 AAACTGCCTCATAGGTTTCTTGTGAGGATCGAAAAAGATGCTTGATATGATTTCACTCTT 10 75421689 158 AAACTGCCTCATAGGTTTCTTGTGAGGATCGATGATGTTAGTGGTTGTAGTGGCTCTTTG 10 75421689 159 GCAATGTGCTATACTGCAGATTCTAAACTCGATGATGTTAGTGGTTGTAGTGGCTCTTTG 10 75419882 160 CTAGAGCTCTGGAGGCCCTGCTGACGGCTCGATGATGTTAGTGGTTGTAGTGGCTCTTTG 10 75433825 161 AAGACTAATTCTGGGCTGTGCCAATTGGTCGATGATGTTAGTGGTTGTAGTGGCTCTTTG 10 75481925 162 CAAAGAGCCACTACAACCACTAACATCATCGAATTTTTGGAAGGCTTGTTATTTGGAAGA 10 75481925 163 CAAAGAGCCACTACAACCACTAACATCATCGAAAAGTTGCAATCATGCTTAATACATAAT 10 75481925 164 CAAGAGAAGACAACATTTATCTGTTATGTCGATGATGTTAGTGGTTGTAGTGGCTCTTTG 10 75481925 165 CAAAGAGCCACTACAACCACTAACATCATCGAGAGAAGCATTTTCCTTTGTTTCTATCTC 10 75481925 166 CAAAGAGCCACTACAACCACTAACATCATCGATGCTTCTGTGGGATAAAAAGTGTAGTTC 10 75481925 167 CAAAGAGCCACTACAACCACTAACATCATCGATAGGAGGCAACTATTAAGAAAGGGCTTT 10 75481925 168 TGATACTTTAAAAAATTTTTTTAAATGATCGATGATGTTAGTGGTTGTAGTGGCTCTTTG 10 75481925 169 CAAAGAGCCACTACAACCACTAACATCATCGAAGTGTTTAGTGAGAGAATCTTTTTTCTT 10 75481925 170 CAAAGAGCCACTACAACCACTAACATCATCGATGTGGAGAATAGCCCATCTTGCTCATTT 10 75481925 171 CAAAGAGCCACTACAACCACTAACATCATCGAAGGTAGAGAGAGAATGCTCTGGGGATGA 10 75481925 172 TTTTAGAGCCTGCCCTCTGTACTCCAAATCGATGATGTTAGTGGTTGTAGTGGCTCTTTG 10 75481925 173 CAAAGAGCCACTACAACCACTAACATCATCGACAAAAAGAAAAATCAGCCTCATAATGCA 10 75481925 174 TGCATTTGTCAAAATTAAGAAATTAACATCGATGATGTTAGTGGTTGTAGTGGCTCTTTG 10 75481925 175 CAAAGAGCCACTACAACCACTAACATCATCGAATGCCCCCATTTGAAAAGAGTTATAATA 10 75481925 176 TTAACTATCCCAAATTCCATTCTCTTTCTCGATGATGTTAGTGGTTGTAGTGGCTCTTTG 10 75481925 177 CAAAGAGCCACTACAACCACTAACATCATCGATTTCAAAGCACTTGTCATACACTCTTTC 10 75481925 178 CAAAGAGCCACTACAACCACTAACATCATCGAGGAAATGAGTATCCTCAAGAGTCTACAC 10 75481925 179 GCTCCAAGACAGGACATGGAGGTGTTCATCGATGATGTTAGTGGTTGTAGTGGCTCTTTG 10 75481925 180 CAAAGAGCCACTACAACCACTAACATCATCGAAAATTTCCGAGACTTCGTTGGCTTTGTT 10 75481925 181 CAAAGAGCCACTACAACCACTAACATCATCGATAAATCTGTTAAAAATGAGCAAAGATCA 10 75481925 182 CTTGACAAGTTCAATCTAAACAAATATATCGATGATGTTAGTGGTTGTAGTGGCTCTTTG 10 75481925 183 CAAAGAGCCACTACAACCACTAACATCATCGATTTTAAAGAGAAACATGGTATTTCACCC 10 75481925 184 CAAAGAGCCACTACAACCACTAACATCATCGAATCAGAGCCTTTGCCAGAATCTGACAGA 10 75481925 185 GTCTTCACATTGCTTCCAACAGTAGTCGTCGATGATGTTAGTGGTTGTAGTGGCTCTTTG 10 75481925 186 CAAAGAGCCACTACAACCACTAACATCATCGACCCCACAAGGCTTAGCAGGGACAAGGTT 10 75481925 187 CCCCTCTTTGAACTCTTCGTTGGAAGTTTCGATGATGTTAGTGGTTGTAGTGGCTCTTTG 10 75481925 188 AGAGAATAGTGTGAGAAATGGTCATCTTTCGAGGAATGAGATGGTCGGTACATGAGAACA 10 76002481 189 TGTTCTCATGTACCGACCATCTCATTCCTCGAGTGAGGCTGTTTTATTTGCTTGGTGCAC 10 75985731 190 GCGCCATGTTAACCGTCAAACGGGTACCTCGATGCTGGTAGATAGGGGAATGGTTCCTGG 3 106480842 191 CTATGTAATCACAGCTTGATGTTCCAATTCGATGCTGGTAGATAGGGGAATGGTTCCTGG 3 106716847 192 AACTACATTAATTAAGAACTTCTGTTCATCGATTTCAGTTTTGAAACTGTAAGAGTAATT 5 95193431

TABLE 33.c6 Probe Location 4 kb Sequence Location N End1 Start2 End2 Chr Start1 End1 Start2 End2 129 26135782 26175106 26175137 28 26131781 26135782 26171136 26175137 130 49908469 49992351 49992382 20 49908438 49912439 49992351 49996352 131 7491275 7547275 7547306 15 7487274 7491275 7547275 7551276 132 27987302 28153765 28153796 19 27983301 27987302 28153765 28157766 133 28081538 28153765 28153796 19 28077537 28081538 28153765 28157766 134 28153796 28173183 28173214 19 28153765 28157766 28173183 28177184 135 20654880 20749766 20749797 13 20650879 20654880 20745796 20749797 136 16316546 16519922 16519953 21 16316515 16320516 16515952 16519953 137 16361936 16519922 16519953 21 16361905 16365906 16515952 16519953 138 16382969 16519922 16519953 21 16378968 16382969 16515952 16519953 139 16389433 16519922 16519953 21 16389402 16393403 16515952 16519953 140 16430421 16519922 16519953 21 16426420 16430421 16515952 16519953 141 47907545 47940508 47940539 1 47907514 47911515 47936538 47940539 142 56337174 56374109 56374140 5 56337143 56341144 56370139 56374140 143 56337174 56519244 56519275 5 56337143 56341144 56515274 56519275 144 30912196 30991768 30991799 26 30908195 30912196 30987798 30991799 145 30912196 30981829 30981860 26 30908195 30912196 30981829 30985830 146 102471878 102533621 102533652 4 102471847 102475848 102529651 102533652 147 10875151 10945798 10945829 11 10875120 10879121 10941828 10945829 148 10907532 10945798 10945829 11 10907501 10911502 10941828 10945829 149 31709566 31731426 31731457 2 31709535 31713536 31731426 31735427 150 31709566 31749361 31749392 2 31709535 31713536 31749361 31753362 151 31709566 31757482 31757513 2 31709535 31713536 31757482 31761483 152 31709566 31759922 31759953 2 31709535 31713536 31759922 31763923 153 31709566 31779719 31779750 2 31709535 31713536 31779719 31783720 154 31709566 31795486 31795517 2 31709535 31713536 31795486 31799487 155 31709566 31816722 31816753 2 31709535 31713536 31816722 31820723 156 31709566 31841824 31841855 2 31709535 31713536 31841824 31845825 157 75421720 75491551 75491582 10 75417719 75421720 75487581 75491582 158 75421720 75481925 75481956 10 75417719 75421720 75481925 75485926 159 75419913 75481925 75481956 10 75419882 75423883 75481925 75485926 160 75433856 75481925 75481956 10 75433825 75437826 75481925 75485926 161 75481956 75505407 75505438 10 75481925 75485926 75501437 75505438 162 75481956 75503397 75503428 10 75481925 75485926 75503397 75507398 163 75481956 75510267 75510298 10 75481925 75485926 75510267 75514268 164 75481956 75518473 75518504 10 75481925 75485926 75514503 75518504 165 75481956 75515462 75515493 10 75481925 75485926 75515462 75519463 166 75481956 75537867 75537898 10 75481925 75485926 75537867 75541868 167 75481956 75558780 75558811 10 75481925 75485926 75558780 75562781 168 75481956 75585674 75585705 10 75481925 75485926 75581704 75585705 169 75481956 75583879 75583910 10 75481925 75485926 75583879 75587880 170 75481956 75598703 75598734 10 75481925 75485926 75598703 75602704 171 75481956 75630159 75630190 10 75481925 75485926 75630159 75634160 172 75481956 75659958 75659989 10 75481925 75485926 75655988 75659989 173 75481956 75657275 75657306 10 75481925 75485926 75657275 75661276 174 75481956 75680755 75680786 10 75481925 75485926 75676785 75680786 175 75481956 75673465 75673496 10 75481925 75485926 75673465 75677466 176 75481956 75698620 75698651 10 75481925 75485926 75694650 75698651 177 75481956 75689296 75689327 10 75481925 75485926 75689296 75693297 178 75481956 75699217 75699248 10 75481925 75485926 75699217 75703218 179 75481956 75711759 75711790 10 75481925 75485926 75707789 75711790 180 75481956 75710114 75710145 10 75481925 75485926 75710114 75714115 181 75481956 75727142 75727173 10 75481925 75485926 75727142 75731143 182 75481956 75737067 75737098 10 75481925 75485926 75733097 75737098 183 75481956 75731193 75731224 10 75481925 75485926 75731193 75735194 184 75481956 75761081 75761112 10 75481925 75485926 75761081 75765082 185 75481956 75769584 75769615 10 75481925 75485926 75765614 75769615 186 75481956 75772669 75772700 10 75481925 75485926 75772669 75776670 187 75481956 75791933 75791964 10 75481925 75485926 75787963 75791964 188 76002512 76079786 76079817 10 75998511 76002512 76075816 76079817 189 75985762 76079786 76079817 10 75985731 75989732 76075816 76079817 190 106480873 106716847 106716878 3 106480842 106484843 106716847 106720848 191 106716878 106947854 106947885 3 106716847 106720848 106943884 106947885 192 95193462 95211956 95211987 5 95193431 95197432 95211956 95215957

TABLE 33.c7 N Probe Primer ID-1 Primer Sequence 129 IGF1_28_26127450_26135782_26165074_26175137_FF OBD RD043.513 ACTTGTAGGTGAGAAAGAAATAGC 130 IL17F_20_49908438_49915179_49992351_49998114_RR OBD RD043.517 CCTGTCTCACCATCTTCTTTTGCCTG 131 IL1R1_15_7480700_7491275_7547275_7554471_FR OBD RD043.521 CCAACTGAACAAGTGAACGCTGCCAG 132 IL1RAP_19_27981648_27987302_28153765_28161424_FR OBD RD043.525 AAATCGGTGAAGAAATGTAGAAAA 133 IL1RAP_19_28069654_28081538_28153765_28161424_FR OBD RD043.529 ATTTCCCCTTGTAGGCTGGTGGC 134 IL1RAP_19_28153765_28161424_28173183_28182762_RR OBD RD043.533 TATGCCAGGGAGGTAGAGCAGCC 135 IL21R_13_20649899_20654880_20738447_20749797_FF OBD RD043.537 GACCTTGTTTTGTTCCCGTGACAGCA 136 IL6ST_21_16316515_16320787_16507936_16519953_RF OBD RD043.541 GCAAAGAGCAATGAGATGTCTATGAT 137 IL6ST_21_16361905_16367133_16507936_16519953_RF OBD RD043.545 AGCCTCTCCCTCCCAGCAAAGCG 138 IL6ST_21_16380568_16382969_16507936_16519953_FF OBD RD043.549 AGCCTCTCCCTCCCAGCAAAGCG 139 IL6ST_21_16389402_16396020_16507936_16519953_RF OBD RD043.553 AGCCTCTCCCTCCCAGCAAAGCG 140 IL6ST_21_16427757_16430421_16507936_16519953_FF OBD RD043.557 TATCAGTCAGCAACTCAGAGGAAC 141 IPMK_1_47907514_47915619_47934069_47940539_RF OBD RD043.561 AGCCAGAGCCTTGCTGTAGTCAG 142 KCND3_5_56337143_56347199_56370847_56374140_RF OBD RD043.565 TGTCCTCCTTTTGCCCCTCCCCT 143 KCND3_5_56337143_56347199_56514669_56519275_RF OBD RD043.569 GCCCTCTGCTTAGTAACCCCTCC 144 KCNE2_26_30910971_30912196_30981829_30991799_FF OBD RD043.573 CCAAAACCCCACCCACGCTGAGC 145 KCNE2_26_30910971_30912196_30981829_30991799_FR OBD RD043.577 TCCAAAACCCCACCCACGCTGAG 146 KCNH2_4_102471847_102478321_102526070_102533652_RF OBD RD043.581 GAGGTCACAGTTCCCTTGTTGGC 147 KCNJ2_11_10875120_10880378_10941535_10945829_RF OBD RD043.585 GGAGGAGTAAATGAATGTTTGTTT 148 KCNJ2_11_10907501_10914338_10941535_10945829_RF OBD RD043.589 CGTAATGAAGCAGACTTTTGGTCAGG 149 KDM1A_2_31709535_31721093_31731426_31738065_RR OBD RD043.593 CCAGCAGATGACAGCAGCAATAAGGG 150 KDM1A_2_31709535_31721093_31749361_31751529_RR OBD RD043.597 CGCCAGCAGATGACAGCAGCAAT 151 KDM1A_2_31709535_31721093_31757482_31759922_RR OBD RD043.601 CGCCAGCAGATGACAGCAGCAAT 152 KDM1A_2_31709535_31721093_31759922_31772142_RR OBD RD043.605 CGCCAGCAGATGACAGCAGCAAT 153 KDM1A_2_31709535_31721093_31779719_31783168_RR OBD RD043.609 CGCCAGCAGATGACAGCAGCAAT 154 KDM1A_2_31709535_31721093_31795486_31798526_RR OBD RD043.613 GCACCTGACAGCAGCACAGACTG 155 KDM1A_2_31709535_31721093_31816722_31820715_RR OBD RD043.617 CGCCAGCAGATGACAGCAGCAAT 156 KDM1A_2_31709535_31721093_31841824_31843977_RR OBD RD043.621 GCACCTGACAGCAGCACAGACTG 157 LAMA2_10_75419882_75421720_75481925_75491582_FF OBD RD043.625 GGATGTTCCAGCCTGAGTTCCTC 158 LAMA2_10_75419882_75421720_75481925_75491582_FR OBD RD043.629 GCTCGCCGTAGCATTCCTCACAC 159 LAMA2_10_75419882_75421720_75481925_75491582_RR OBD RD043.633 CAACCTATTGCCGATGCCCTCAAACT 160 LAMA2_10_75433825_75441819_75481925_75491582_RR OBD RD043.637 CCTACTACAACCTATTGCCGATGCCC 161 LAMA2_10_75481925_75491582_75503397_75505438_RF OBD RD043.641 GCCGATGCCCTCAAACTATTTATCAA 162 LAMA2_10_75481925_75491582_75503397_75505438_RR OBD RD043.645 GCAAAGGACCCAACATCGTAGGC 163 LAMA2_10_75481925_75491582_75510267_75513025_RR OBD RD043.649 GCAAAGGACCCAACATCGTAGGC 164 LAMA2_10_75481925_75491582_75515462_75518504_RF OBD RD043.653 GCTCGCCGTAGCATTCCTCACAC 165 LAMA2_10_75481925_75491582_75515462_75518504_RR OBD RD043.657 TGTGATTGATAGGACTGCTTTGAGGC 166 LAMA2_10_75481925_75491582_75537867_75543336_RR OBD RD043.661 TTGTGTTTGAGTCTGGCTTGTCTAAT 167 LAMA2_10_75481925_75491582_75558780_75560310_RR OBD RD043.665 GCAAAGGACCCAACATCGTAGGC 168 LAMA2_10_75481925_75491582_75583879_75585705_RF OBD RD043.669 CAACCTATTGCCGATGCCCTCAAACT 169 LAMA2_10_75481925_75491582_75583879_75585705_RR OBD RD043.673 CTACAACCTATTGCCGATGCCCTC 170 LAMA2_10_75481925_75491582_75598703_75603065_RR OBD RD043.677 GGCTTAGGGCATTGGTTAGGAGC 171 LAMA2_10_75481925_75491582_75630159_75632019_RR OBD RD043.681 TCTCTCTGTTTCTCAGTTCTATCGC 172 LAMA2_10_75481925_75491582_75657275_75659989_RF OBD RD043.685 ATCATTGAAGTTAGAAAAGGTCTT 173 LAMA2_10_75481925_75491582_75657275_75659989_RR OBD RD043.689 GCAAAGGAATGCCAACTGCCAGC 174 LAMA2_10_75481925_75491582_75673465_75680786_RF OBD RD043.693 CCTTTACCCAACTCCCACTGAGG 175 LAMA2_10_75481925_75491582_75673465_75680786_RR OBD RD043.697 CCTACTACAACCTATTGCCGATGCCC 176 LAMA2_10_75481925_75491582_75689296_75698651_RF OBD RD043.701 GCAAAGGACCCAACATCGTAGGC 177 LAMA2_10_75481925_75491582_75689296_75698651_RR OBD RD043.705 CTGATTTGTGGGCATCGTCTACAGTT 178 LAMA2_10_75481925_75491582_75699217_75700676_RR OBD RD043.709 GCAAAGGACCCAACATCGTAGGC 179 LAMA2_10_75481925_75491582_75710114_75711790_RF OBD RD043.713 CGAGGGAGAGAGTAAAGCCAACC 180 LAMA2_10_75481925_75491582_75710114_75711790_RR OBD RD043.717 CCTACTACAACCTATTGCCGATGCCC 181 LAMA2_10_75481925_75491582_75727142_75730779_RR OBD RD043.721 TCAGGTAGCACTCTTATCTTTCCAGA 182 LAMA2_10_75481925_75491582_75731193_75737098_RF OBD RD043.725 TAGGGAGTTGGCACTGGCACTTTT 183 LAMA2_10_75481925_75491582_75731193_75737098_RR OBD RD043.729 GCTCGCCGTAGCATTCCTCACAC 184 LAMA2_10_75481925_75491582_75761081_75765848_RR OBD RD043.733 CAGGAAGACTTTATTATGGAATGCGT 185 LAMA2_10_75481925_75491582_75767487_75769615_RF OBD RD043.737 CCTACTACAACCTATTGCCGATGCCC 186 LAMA2_10_75481925_75491582_75772669_75776905_RR OBD RD043.741 CTTGAAACCTGACAAAGATACCAGC 187 LAMA2_10_75481925_75491582_75789669_75791964_RF OBD RD043.745 TTCCATTCCAAGATTGATGAAAAT 188 LAMA2_10_75985731_76002512_76077151_76079817_FF OBD RD043.749 GCAGACACAAGCAAGTAAATAGACAA 189 LAMA2_10_75985731_76002512_76077151_76079817_RF OBD RD043.753 CCTACTACAACCTATTGCCGATGCCC 190 LDB2_3_106480842_106484500_106716847_106728445_RR OBD RD043.757 GCACAGAATAGTCTCCCAAATAGTTTAT 191 LDB2_3_106716847_106728445_106944178_106947885_RF OBD RD043.761 AGTGAAGGAGGAGAGTCATCTGCT 192 LEPR_5_95193431_95200537_95211956_95218723_RR OBD RD043.765 GAGCCAAACCATAAAGAGAAAGACTG

TABLE 33.c8 N Primer ID-2 Primer Sequence Probe Marker 129 OBD RD043.515 TCCATAAACAGGTGAGGAAGACAC IGF1 OBD RD043.513.515 130 OBD RD043.519 TTAGTCTCTTTCTTCAGATGGCTATC IL17F OBD RD043.517.519 131 OBD RD043.523 ACAACGAGGACTCAGATTTCTCAGAG IL1R1 OBD RD043.521.523 132 OBD RD043.527 GCAAGTTAGTGGTTGAGATTGGAT IL1RAP OBD RD043.525.527 133 OBD RD043.531 TATGCCAGGGAGGTAGAGCAGCC IL1RAP OBD RD043.529.531 134 OBD RD043.535 GCTTGACTTGCTCTGGGAGGAGA IL1RAP OBD RD043.533.535 135 OBD RD043.539 CTAATAAACTCAGCGAGGCAGCAGGA IL21R OBD RD043.537.539 136 OBD RD043.543 AGCCTCTCCCTCCCAGCAAAGCG IL6ST OBD RD043.541.543 137 OBD RD043.547 GCCTCAGAAAGAGTTGTAGTTATTGT IL6ST OBD RD043.545.547 138 OBD RD043.551 CAGTTTTGTAGAGCACCTGATTAGAA IL6ST OBD RD043.549.551 139 OBD RD043.555 GGGCTCTACTCAGTGATTGCCTG IL6ST OBD RD043.553.555 140 OBD RD043.559 AGCCTCTCCCTCCCAGCAAAGCG IL6ST OBD RD043.557.559 141 OBD RD043.563 GCCATCAGTGACCAAGGCACCTC IPMK OBD RD043.561.563 142 OBD RD043.567 ATCAGAGGGTGGTTATGTCGGGC KCND3 OBD RD043.565.567 143 OBD RD043.571 ATCAGAGGGTGGTTATGTCGGGC KCND3 OBD RD043.569.571 144 OBD RD043.575 GGGTCAGGTTGGTGAGAGAAGGG KCNE2 OBD RD043.573.575 145 OBD RD043.579 ATGGATGGTGGATGGTGGGAACC KCNE2 OBD RD043.577.579 146 OBD RD043.583 TTCCACCCCGTCCCCATCTTCAC KCNH2 OBD RD043.581.583 147 OBD RD043.587 AAGAGTAATCTGCTTGGTAAATAG KCNJ2 OBD RD043.585.587 148 OBD RD043.591 CTACTTGAAGAAATAAGCCTTGCTGC KCNJ2 OBD RD043.589.591 149 OBD RD043.595 CCACTTTATGAAGCAAATGGACAAGC KDM1A OBD RD043.593.595 150 OBD RD043.599 CCCTTCTCTCTGTTGCTGCCGTG KDM1A OBD RD043.597.599 151 OBD RD043.603 GCTCGCAGGTGCTGGGAATACAG KDM1A OBD RD043.601.603 152 OBD RD043.607 TGGTGTCTCAGGCTTGGCAGCAG KDM1A OBD RD043.605.607 153 OBD RD043.611 GAGAGAGCCCAGGTTAGACAGCG KDM1A OBD RD043.609.611 154 OBD RD043.615 AAACAAAGCCAGGGAGGAGGACG KDM1A OBD RD043.613.615 155 OBD RD043.619 GCCAGAAAGGAAGGTGGGAGCCT KDM1A OBD RD043.617.619 156 OBD RD043.623 CCACTACTCTCATAGGGAGGGAG KDM1A OBD RD043.621.623 157 OBD RD043.627 GCTCGCCGTAGCATTCCTCACAC LAMA2 OBD RD043.625.627 158 OBD RD043.631 GGCTTCAACCGTCTCCAAGGCTT LAMA2 OBD RD043.629.631 159 OBD RD043.635 TTCTGTAGAGCCTCACCAACACTGTG LAMA2 OBD RD043.633.635 160 OBD RD043.639 CGACTTCTCGGTTGTTTAGCATCACA LAMA2 OBD RD043.637.639 161 OBD RD043.643 CGTGACAGCAGTTTTATTGTTTGGG LAMA2 OBD RD043.641.643 162 OBD RD043.647 GGACCCGAGCACCACTCTTGAGA LAMA2 OBD RD043.645.647 163 OBD RD043.651 TCCCAGAACAGCCAGCACAGCAG LAMA2 OBD RD043.649.651 164 OBD RD043.655 GTGACTGCCAGGTTTGCCACCAA LAMA2 OBD RD043.653.655 165 OBD RD043.659 CCTACTACAACCTATTGCCGATGCCC LAMA2 OBD RD043.657.659 166 OBD RD043.663 CGATGCCCTCAAACTATTTATCAAAG LAMA2 OBD RD043.661.663 167 OBD RD043.667 GACCACACACCAGGAGGCTGATG LAMA2 OBD RD043.665.667 168 OBD RD043.671 CCACTATTTCCACACCACACAGTCTG LAMA2 OBD RD043.669.671 169 OBD RD043.675 TGGCACTCCTCCTCGTCATCAGG LAMA2 OBD RD043.673.675 170 OBD RD043.679 GCTCGCCGTAGCATTCCTCACAC LAMA2 OBD RD043.677.679 171 OBD RD043.683 ACATAAAGAACACTCTATCCAAAA LAMA2 OBD RD043.681.683 172 OBD RD043.687 TTCGCAAAGGACCCAACATCGTAG LAMA2 OBD RD043.685.687 173 OBD RD043.691 GCTCGCCGTAGCATTCCTCACAC LAMA2 OBD RD043.689.691 174 OBD RD043.695 GCTCGCCGTAGCATTCCTCACAC LAMA2 OBD RD043.693.695 175 OBD RD043.699 TCGCTGAGGAGCATCCAACTTGATTA LAMA2 OBD RD043.697.699 176 OBD RD043.703 CTGTCAACGGGATGTGAGGTCAGC LAMA2 OBD RD043.701.703 177 OBD RD043.707 CCTACTACAACCTATTGCCGATGCCC LAMA2 OBD RD043.705.707 178 OBD RD043.711 CTCAGCAGGAAATCGCCCTCCAG LAMA2 OBD RD043.709.711 179 OBD RD043.715 GCTCGCCGTAGCATTCCTCACAC LAMA2 OBD RD043.713.715 180 OBD RD043.719 GCTCCAACACAACCCAGTTATTTCTG LAMA2 OBD RD043.717.719 181 OBD RD043.723 CCTACTACAACCTATTGCCGATGCCC LAMA2 OBD RD043.721.723 182 OBD RD043.727 CCTACTACAACCTATTGCCGATGCCC LAMA2 OBD RD043.725.727 183 OBD RD043.731 GACCCAAAGCAGAGAGGCAACTG LAMA2 OBD RD043.729.731 184 OBD RD043.735 CAACCTATTGCCGATGCCCTCAAACT LAMA2 OBD RD043.733.735 185 OBD RD043.739 TAGGGAACCGACTGAATCTGATACAG LAMA2 OBD RD043.737.739 186 OBD RD043.743 CAATACTTTAGAGTCACATCTCGTGC LAMA2 OBD RD043.741.743 187 OBD RD043.747 GTGTGTAAGTTCTAAGTGTTTATTA LAMA2 OBD RD043.745.747 188 OBD RD043.751 CAACCTATTGCCGATGCCCTCAAACT LAMA2 OBD RD043.749.751 189 OBD RD043.755 CAACCCAAAGCAATCCAGCAAAGCAT LAMA2 OBD RD043.753.755 190 OBD RD043.759 GATGTTTCTTATTTTGAGTTTTCCCAGG LDB2 OBD RD043.757.759 191 OBD RD043.763 GTCATCATTTATGTGGAAGGAATA LDB2 OBD RD043.761.763 192 OBD RD043.767 AACCCTGTCATAAGTTGAAGAAGAGC LEPR OBD RD043.765.767

TABLE 33.d1 N Probe GeneLocus Probe_Count_Total Probe_Count_Sig 193 LMO7_17_48756745_48760926_48985578_48994371_FR LMO7 1 47 194 LY6D_9_81540380_81548206_81579682_81590550_FR LY6D 2 31 195 LY6D_9_81540380_81548206_81579682_81590550_RR LY6D 2 31 196 MAP3K4_31_2786762_2795002_2851292_2856203_FR MAP3K4 1 31 197 MAP3K9_24_16803396_16807626_16910389_16918093_RF MAP3K9 1 29 198 MAPK1_8_3352241_3355955_3404723_3412822_RR MAPK1 3 31 199 MAPK1_8_3435741_3439526_3469888_3479148_FF MAPK1 3 31 200 MAPK1_8_3435741_3439526_3469888_3479148_FR MAPK1 3 31 201 MAPK3_13_19583177_19588616_19608792_19619090_FF MAPK3 1 31 202 MAPK9_14_2229196_2237168_2274036_2279957_RR MAPK9 2 38 203 MAPK9_14_2229196_2237168_2401910_2410518_RR MAPK9 2 38 204 MDH1_15_37903511_37909683_38029907_38037711_RR MDH1 2 125 205 MDH1_15_37903511_37909683_38069969_38081007_RR MDH1 2 125 206 MDM4_5_1002213_1010298_1034976_1038480_FF MDM4 1 31 207 MED25_10_19508221_19515457_19591613_19593754_RF MED25 1 30 208 MEF2A_1_104992073_105002150_105161756_105164976_RF MEF2A 1 181 209 MIPEP_17_4332285_4337643_4521242_4528379_FF MIPEP 3 131 210 MIPEP_17_4413535_4418797_4506914_4517925_FF MIPEP 3 131 211 MIPEP_17_4413535_4418797_4521242_4528379_FF MIPEP 3 131 212 MMP1_7_12601995_12610418_12711728_12717668_RF MMP1 2 33 213 MMP1_7_12711728_12717668_12737470_12745025_FR MMP1 2 33 214 MS4A2_12_19894956_19896244_19962410_19974828_RF MS4A2 2 112 215 MS4A2_12_19992086_20002065_20049543_20053548_RF MS4A2 2 112 216 MSI2_11_31942510_31947907_32032038_32042221_RR MSI2 3 204 217 MSI2_11_31953015_31955643_32032038_32042221_RF MSI2 3 204 218 MSI2_11_31953015_31955643_32032038_32042221_RR MSI2 3 204 219 MSTN_18_66448734_66450075_66490497_66500489_FF MSTN 1 50 220 MTHFR_2_39760745_39767847_39804925_39808549_FR MTHFR 3 29 221 MTHFR_2_39760745_39767847_39835824_39839260_FF MTHFR 3 29 222 MTHFR_2_39760745_39767847_39835824_39839260_FR MTHFR 3 29 223 MTMR3_8_6868138_6874813_6923181_6926871_RR MTMR3 1 31 224 MYBPC2_10_20037236_20038811_20080873_20084086_RF MYBPC2 1 31 225 MYH1_11_52882980_52886797_52907287_52915321_RF MYH1 1 50 226 MYL1_6_1098854_1104299_989242_996235_RR MYL1 1 44 227 MYL4_11_17193641_17194702_17358881_17368963_RF MYL4 6 34 228 MYL4_11_17206623_17211708_17358881_17368963_RF MYL4 6 34 229 MYL4_11_17246461_17251113_17358881_17368963_RF MYL4 6 34 230 MYL4_11_17257199_17259878_17358881_17368963_RF MYL4 6 34 231 MYL4_11_17267739_17271299_17358881_17368963_RF MYL4 6 34 232 MYL4_11_17290815_17294484_17358881_17368963_RF MYL4 6 34 233 MYOZ1_1_61314759_61323626_61385709_61392305_FF MYOZ1 3 109 234 MYOZ1_1_61323626_61338801_61385709_61392305_FF MYOZ1 3 109 235 MYOZ1_1_61350438_61357018_61385709_61392305_RF MYOZ1 3 109 236 NDN_1_109635329_109640204_109733366_109741347_RF NDN 3 31 237 NDN_1_109711483_109720818_109733366_109741347_RF NDN 3 31 238 NDN_1_109733366_109741347_109779877_109789352_FR NDN 3 31 239 NDUFA8_25_25717207_25721463_25884535_25891335_FR NDUFA8 1 31 240 NEUROD2_11_22762666_22765277_22824653_22836914_FR NEUROD2 1 35 241 NFIB_23_34300375_34312881_34537544_34541097_RF NFIB 2 195 242 NFIB_23_34364872_34370510_34413070_34423547_FR NFIB 2 195 243 NPPA_2_39707018_39708108_39760745_39767847_RF NPPA 4 31 244 NPPA_2_39714609_39718671_39760745_39767847_FF NPPA 4 31 245 NPPA_2_39714609_39718671_39760745_39767847_RF NPPA 4 31 246 NPPA_2_39741527_39742701_39760745_39767847_RF NPPA 4 31 247 PALLD_2_66194319_66195345_66291709_66310979_FF PALLD 5 288 248 PALLD_2_66194319_66195345_66291709_66310979_FR PALLD 5 288 249 PALLD_2_66212034_66222303_66449615_66454401_FF PALLD 5 288 250 PALLD_2_66291709_66310979_66324859_66327343_FR PALLD 5 288 251 PALLD_2_66291709_66310979_66449615_66454401_RF PALLD 5 288 252 PCBP4_16_35681721_35687901_35707118_35711409_FF PCBP4 2 31 253 PCBP4_16_35681721_35687901_35729420_35734814_FF PCBP4 2 31 254 PHOSPHO1_11_25089999_25092180_25214955_25221072_RR PHOSPHO1 2 30 255 PHOSPHO1_11_25177016_25183355_25214955_25221072_RR PHOSPHO1 2 30 256 PIK3R1_21_5606382_5618174_5697527_5698879_RF PIK3R1 1 44

TABLE 33.d2 N HyperG_Stats FDR_HyperG Percent_Sig logFC AveExpr 193 0.264202412 0.310300562 2.13 0.308955 8.756434343 194 0.024599258 0.075554863 6.45 −0.510502405 10.21074765 195 0.024599258 0.075554863 6.45 −0.475839307 10.73785324 196 0.198752749 0.267074007 3.23 −0.262976484 8.919564336 197 0.189010904 0.267074007 3.45 −0.180023399 10.17483943 198 0.001955877 0.014841655 9.68 −0.189403578 11.32640428 199 0.001955877 0.014841655 9.68 −0.357643779 9.43283737 200 0.001955877 0.014841655 9.68 −0.455473419 9.347542263 201 0.198752749 0.267074007 3.23 −0.414926364 10.40126841 202 0.035117143 0.100669145 5.26 −0.304638764 10.45869573 203 0.035117143 0.100669145 5.26 −0.350361266 10.09820875 204 0.189650589 0.267074007 1.6 −0.39554798 7.948266107 205 0.189650589 0.267074007 1.6 −0.352490885 8.366984869 206 0.198752749 0.267074007 3.23 −0.184406239 9.603449014 207 0.193928419 0.267074007 3.33 −1.002322155 9.303488712 208 0.337499771 0.365861096 0.55 −0.268195094 9.66649256 209 0.070335458 0.151221234 2.29 0.181091948 9.982716815 210 0.070335458 0.151221234 2.29 −0.243481105 10.43396472 211 0.070335458 0.151221234 2.29 −0.262461763 10.1207347 212 0.027478161 0.080560972 6.06 −0.363422404 9.195426411 213 0.027478161 0.080560972 6.06 −0.344950706 9.351822484 214 0.169245181 0.267074007 1.79 −0.432136877 12.0727133 215 0.169245181 0.267074007 1.79 −0.227521522 9.522194245 216 0.147248814 0.267074007 1.47 0.571287251 9.737071247 217 0.147248814 0.267074007 1.47 −0.250081475 9.240013839 218 0.147248814 0.267074007 1.47 −0.454717411 10.26002015 219 0.274219102 0.310300562 2 0.301875352 8.089384778 220 0.001616117 0.014841655 10.34 −0.275284765 10.54722144 221 0.001616117 0.014841655 10.34 −0.290761819 10.35745977 222 0.001616117 0.014841655 10.34 −0.323026508 10.39283037 223 0.198752749 0.267074007 3.23 −0.306058656 10.27824044 224 0.198752749 0.267074007 3.23 0.218360553 10.39432728 225 0.274219102 0.310300562 2 −0.340884422 11.66695629 226 0.253514025 0.310300562 2.27 −0.590441109 8.581505532 227 0.000000311818145952167 0.0000201122704139147 17.65 0.269287734 9.380557343 228 0.000000311818145952167 0.0000201122704139147 17.65 0.204015501 9.601273444 229 0.000000311818145952167 0.0000201122704139147 17.65 0.256704897 9.061911736 230 0.000000311818145952167 0.0000201122704139147 17.65 0.183545822 10.10564073 231 0.000000311818145952167 0.0000201122704139147 17.65 0.205055848 10.06240784 232 0.000000311818145952167 0.0000201122704139147 17.65 0.220380659 9.12627111 233 0.048283923 0.124572522 2.75 −0.212727454 10.43860627 234 0.048283923 0.124572522 2.75 −0.281776187 9.409288269 235 0.048283923 0.124572522 2.75 −0.492368455 10.04957678 236 0.001955877 0.014841655 9.68 −0.340662221 9.476696148 237 0.001955877 0.014841655 9.68 −0.43400853 9.302335644 238 0.001955877 0.014841655 9.68 −0.3910292 9.299496898 239 0.198752749 0.267074007 3.23 0.253713189 8.751509754 240 0.217141868 0.285829602 2.86 −0.204232609 12.1874556 241 0.260374827 0.310300562 1.03 0.324297214 8.32941724 242 0.260374827 0.310300562 1.03 −0.228545891 7.918191482 243 0.000112254 0.002068688 12.9 −0.235040273 10.43931511 244 0.000112254 0.002068688 12.9 −0.298128772 9.961402566 245 0.000112254 0.002068688 12.9 −0.196073384 11.28835418 246 0.000112254 0.002068688 12.9 −0.358964974 10.23538918 247 0.057376468 0.137915817 1.74 −0.331113386 8.504927574 248 0.057376468 0.137915817 1.74 −0.333004015 8.42257663 249 0.057376468 0.137915817 1.74 0.337185069 9.542961911 250 0.057376468 0.137915817 1.74 −0.19420402 10.03309215 251 0.057376468 0.137915817 1.74 0.285252571 10.1390655 252 0.024599258 0.075554863 6.45 −0.606928989 7.90009089 253 0.024599258 0.075554863 6.45 −0.5741059 7.791564161 254 0.023201487 0.075554863 6.67 −0.435541833 8.652187929 255 0.023201487 0.075554863 6.67 −0.452293144 9.746122909 256 0.253514025 0.310300562 2.27 −0.222099166 10.2584473

TABLE 33.d3 N t P.Value adj.P.Val B FC 193 5.578062929 0.0000217701905479979 0.004204233 2.8863206 1.238810056 194 −8.542517182 0.0000000596329188972969 0.000077542672206118 8.396017365 0.701977938 195 −5.419897283 0.0000307827940531150 0.005054403 2.556989182 0.719048353 196 −5.295421974 0.0000405075194431574 0.006131956 2.295788713 0.833366791 197 −5.303171478 0.0000398191777050705 0.006067758 2.312100067 0.88268868 198 −5.26401715 0.0000434237366404068 0.006490268 2.229621301 0.876968192 199 −7.362483567 0.000000542792493499413 0.00033823 6.362585392 0.780438157 200 −6.920589559 0.00000130208881243147 0.000596309 5.545829579 0.729270823 201 −6.507834204 0.00000301932875673387 0.001051643 4.755925321 0.750057777 202 −5.2522991 0.0000445660037600909 0.006607886 2.204905558 0.809644918 203 −6.955664773 0.00000121355337901372 0.00057037 5.611759271 0.784387655 204 −5.962344466 0.00000949692524861803 0.002437336 3.673443959 0.760200574 205 −6.959876235 0.00000120334955772376 0.00057037 5.619662717 0.783230643 206 −5.197233953 0.0000503586344752859 0.007169673 2.088570872 0.880011182 207 −11.12974035 0.000000000855760191439498 0.00000370924500756165 12.15128673 0.49919585 208 −6.217777769 0.00000552671615692750 0.001607736 4.185638781 0.830357728 209 5.017111985 0.0000752584737618864 0.009531926 1.705942088 1.133741668 210 −6.41916147 0.00000362800718522512 0.001213128 4.582892014 0.844704648 211 −6.682538446 0.00000210909449126610 0.000822758 5.093407671 0.833664171 212 −5.560509533 0.0000226203345689378 0.004245102 2.849918149 0.777318413 213 −5.730820553 0.0000156218240048023 0.003423637 3.201499442 0.787334878 214 −5.520053358 0.0000247115601581872 0.004416684 2.76587789 0.741163183 215 −6.250406563 0.00000516052782800820 0.001572751 4.250401752 0.854100935 216 10.84451596 0.00000000131747089617564 0.00000513945396598118 11.78059039 1.485848734 217 −5.219666256 0.0000479113597540456 0.006948038 2.136000723 0.840848928 218 −7.685287888 0.000000291255727507992 0.000248829 6.940120692 0.72965308 219 6.038727238 0.00000807050267149696 0.002138121 3.82756083 1.232745812 220 −5.887655696 0.0000111429983778881 0.002634475 3.521975599 0.826287206 221 −5.456068621 0.0000284312776732711 0.004832995 2.632564179 0.817470277 222 −6.439861138 0.00000347543587764876 0.00118927 4.623388743 0.799391142 223 −7.58351219 0.000000353881586378611 0.000270685 6.759774473 0.808848462 224 5.073968482 0.0000662731427137706 0.008670693 1.827052816 1.16341076 225 −8.114538033 0.000000130057060380918 0.000126838 7.683168577 0.789557138 226 −8.247664393 0.000000101785970767585 0.000104491 7.907878402 0.664139813 227 5.610514627 0.0000202836082244147 0.0039679 2.953520209 1.205212661 228 5.212827288 0.0000486443312060846 0.007002271 2.121546166 1.151900019 229 5.148455682 0.0000561297752836139 0.007709938 1.985261129 1.194746794 230 5.217277153 0.0000481661245096288 0.006959113 2.130951759 1.135671685 231 5.625048666 0.0000196519236843458 0.003951657 2.983574644 1.152730969 232 5.403530817 0.0000319112455916194 0.005171517 2.522744449 1.165040945 233 −5.566335209 0.0000223344813272804 0.004245102 2.862003659 0.862904344 234 −5.636876017 0.0000191527686471659 0.003891404 3.008012687 0.82257767 235 −7.033201866 0.00000103922865236368 0.000532857 5.756832398 0.710857134 236 −6.838387929 0.00000153671624367046 0.000651601 5.390579615 0.789678753 237 −8.482004556 0.0000000664881274369185 0.000078597025797400 8.296903933 0.740202273 238 −8.714888103 0.0000000438512643767021 0.000068425512933406 8.675347723 0.762585392 239 5.20108882 0.0000499291851743305 0.0071608 2.09672508 1.192271822 240 −5.785373903 0.0000138850583130889 0.00313096 3.313338935 0.868000266 241 5.491634267 0.0000262980290948125 0.004539319 2.706725558 1.252054372 242 −5.2300823 0.0000468165952760807 0.00681461 2.158006387 0.853494705 243 −5.382789941 0.0000334023098752759 0.005277635 2.479303216 0.84966128 244 −5.150382787 0.0000558894507041173 0.007704055 1.98934712 0.813306601 245 −5.523154669 0.0000245444648394958 0.004416684 2.772327241 0.872923188 246 −6.676552256 0.00000213503855287626 0.000824632 5.081919838 0.779723773 247 −5.77339837 0.0000142485411810267 0.003153542 3.288821006 0.794922773 248 −6.210571382 0.00000561113691758904 0.001609489 4.171314668 0.793881722 249 6.879077809 0.00000141555716527236 0.000606823 5.467557689 1.263289306 250 −5.639859813 0.0000190289062701250 0.00388648 3.01417515 0.874055006 251 5.102219822 0.0000622226113504969 0.008370014 1.887120126 1.218623588 252 −4.99093597 0.0000798030028297843 0.009820552 1.65008659 0.65659288 253 −5.313651741 0.0000389072312178752 0.005987456 2.334148884 0.671702405 254 −10.36202183 0.00000000278690058103200 0.00000836284551277371 11.13041085 0.739416 255 −9.587137852 0.00000000979318467345839 0.000020106954426927 10.02246539 0.7308802 256 −5.143048179 0.0000568097724220449 0.007775962 1.973793794 0.857317105

TABLE 33.d4 Loop Probe sequence N FC_1 LS Detected 60 mer 193 1.238810056 1 Sprinter AATATTTCTTTAAGACTAATTGTTCTACTCGAGGCATTAAATACTTTCCCTCTAGCCAGC 194 −1.424546194 −1 Stayer CAGAATCTCTCTGCTTAATGGGCCCATATCGACAGCTTAACGGATTTTCACAGAGTACAC 195 −1.390727058 −1 Stayer CATTGGAGTGGAATAGAGAGCTTATAAATCGACAGCTTAACGGATTTTCACAGAGTACAC 196 −1.199951823 −1 Stayer GACCCTATGCTCCITTCCTGGAACATCATCGAGATGTATGACAACAAATGCCAGTATTTA 197 −1.132902259 −1 Stayer TAACCAAACCATAGTGTGAAAACAGCTTTCGATATGTAATTTTATTAAGAATATTATTTT 198 −1.140292212 −1 Stayer GAATGGGTACTCTGCTGGAAAGTTGATTTCGAGGTGAAAGCCGAGGGAAGTGAGTAGCCA 199 −1.281331507 −1 Stayer TTGGGTACTAGAACCCTTACAGCTCCITTCGATAAGAATGCCAGGATCTTTTGCTGGGGA 200 −1.3712327 −1 Stayer TTGGGTACTAGAACCCTTACAGCTCCITTCGACAAATCTATGATATCAAGAATAACTAAC 201 −1.333230627 −1 Stayer TAACATGCTCAGTAAATGCTACCTGTGGTCGAGCTTTTCTTATCCATGCTTCAGGGGTGA 202 −1.23510934 −1 Stayer ATCCCTGTACTCCTGTGACCAGGGCACGTCGAGCTTTCAACTGAAACTTAGGATTTTGGA 203 −1.27487983 −1 Stayer ATCCCTGTACTCCTGTGACCAGGGCACGTCGATTAATATAATACATCACATTAACAGAAT 204 −1.315442311 −1 Stayer CAAAAAATGCACTCTTTCAAAGAATCTCTCGAAAAGCAAGATCCTTCTTTTAATGGAATT 205 −1.276763121 −1 Stayer CAAAAAATGCACTCTTTCAAAGAATCTCTCGATTCAGTGTGATTGGAATCATGGAAGGAG 206 −1.136349196 −1 Stayer TTAAACAACAAAACCCAACAGAGGAAATTCGACACTTACCACAATGAGGTGGATGCCTTC 207 −2.003221783 −1 Stayer GTCACTGCCTTCAAACCTTATGGTACGATCGAGAAGCTAAAACAAGTATAAATATATATG 208 −1.204300227 −1 Stayer CTGCTGTTTACTCAATATCATGACAATTTCGACTGGTAAATATGGTAACCCCAAAGCAAT 209 1.133741668 1 Sprinter TTGTCACAGTGTAGTGAGGAGATAAATATCGAAGAGGATAAACTGGTCCCTGCACAGTCT 210 −1.183845741 −1 Stayer GTTACAACCCCTGACATGAAAAAGGTACTCGATGCTGGGTTTGAGTAACGCTGGAGCTGC 211 −1.199523783 −1 Stayer GTTACAACCCCTGACATGAAAAAGGTACTCGAAGAGGATAAACTGGTCCCTGCACAGTCT 212 −1.286474093 −1 Stayer ACAGTAAAGGTGTTTTGGACTTATTGGCTCGATGTTAAAGAATAGTTCTATTCTACTTTG 213 −1.270107585 −1 Stayer ACAGTAAAGGTGTTTTGGACTTATTGGCTCGAAATATATTATGATGTACCTCTGAAAAAA 214 −1.349230538 −1 Stayer TGTGTTTTACTTTTAATGGAGTTGCTGTTCGAGAGTGGTGTGTTAGCTCTCCGCCTTGGG 215 −1.170821807 −1 Stayer TAAGTCTCTTCTGAAAAAAAATAGCAGGTCGAATCCAATCACATTTGCGAATGCCCTTCA 216 1.485848734 1 Sprinter ATTGTGCGCAAAGGAAATTATTCTAAGATCGAACACTGTTCAGCTCTTTTGTCTGGTGAT 217 −1.189274276 −1 Stayer AACCAGACTGATGTTAACATCGCCACGTTCGAGTACCTGTGCTCAGCAACAAGATGGCTT 218 −1.370514328 −1 Stayer AAGCCATCTTGTTGCTGAGCACAGGTACTCGAACACTGTTCAGCTCTTTTGTCTGGTGAT 219 1.232745812 1 Sprinter AAATCAGAGAGACACTCTCTGGATGGTCTCGAACACTAGATCTTTGAGTCTAGTCTCTTT 220 −1.210232946 −1 Stayer GAGTCTCTAGGTACCTGTCCGCTTCAGGTCGAGCATCTGGACTAATTTGTCCCGAGCTGC 221 −1.223286066 −1 Stayer GAGTCTCTAGGTACCTGTCCGCTTCAGGTCGATAGAAATGAAGAGCTCAGCTGGGTGGCT 222 −1.250952065 −1 Stayer GAGTCTCTAGGTACCTGTCCGCTTCAGGTCGATTTGGAGATGGTTGTACAATGCTATAAA 223 −1.236325525 −1 Stayer AGGAAATGAACATCTAAATTCAAGAAGCTCGACAGTACTAGAAACCAACCCCTTCTCCCC 224 1.16341076 1 Sprinter CTATTTCATGCTACGCCCTTGGGCTTTATCGAGAGTCTGCTGAATTTGTCTGCCACCTCT 225 −1.266532784 −1 Stayer TAATTAAAATTTGATAATAAAGGCCTACTCGATGCCCTCCTTCTTGTACTCCTCCTGCTC 226 −1.505707053 −1 Stayer CCTCCAGGAATTCTGTTAAGATGTATTTTCGAGTTAGAAAATTCCCCTCTATTTGTAGTT 227 1.205212661 1 Sprinter ATAAAAAGCAAATAAGTGCTAGTGTTACTCGAAAAGTTGGCAGGTCTTAATCTACTGGAT 228 1.151900019 1 Sprinter ATAAAAAGCAAATAAGTGCTAGTGTTACTCGAGGCTTACATTTCATCTGGGAAGTTTTTC 229 1.194746794 1 Sprinter ATAAAAAGCAAATAAGTGCTAGTGTTACTCGAATACCACGTTTACTCAGACAAGAGAAAC 230 1.135671685 1 Sprinter ATAAAAAGCAAATAAGTGCTAGTGTTACTCGAGCCTGTTGGGCGTGAGATAATCACCTTC 231 1.152730969 1 Sprinter ATAAAAAGCAAATAAGTGCTAGTGTTACTCGAGCCTCCAGAACTCTGAGGAATAAATGTC 232 1.165040945 1 Sprinter ATAAAAAGCAAATAAGTGCTAGTGTTACTCGAATTTCGTTTCTGCTAGTGCTTTAGCACA 233 −1.158877003 −1 Stayer ATGTCCAGAGAATGGAAACAAACCTGACTCGAGGAATACGTGGGAAGAAATGGGGTACAG 234 −1.215690672 −1 Stayer AATAACCAACATAACTAGAAAATTCTCCTCGAGGAATACGTGGGAAGAAATGGGGTACAG 235 −1.40675243 −1 Stayer CTGTACCCCATTTCTTCCCACGTATTCCTCGAGAGCTATATCAAAAAGATTTTGGTATTT 236 −1.266337731 −1 Stayer GACAGGGGTCTAGAATCATAGATTTCCCTCGATCTTGAGGTTGACAGTTACCACAATTAT 237 −1.350982072 −1 Stayer GACAGGGGTCTAGAATCATAGATTTCCCTCGAATATGTAGTTGAGTCAGATCTGGGATTT 238 −1.311328555 −1 Stayer GACAGGGGTCTAGAATCATAGATTTCCCTCGATACCCCAGTTTTCTTTTTGATCCCTTCA 239 1.192271822 1 Sprinter GCTTCCAGAAATGAGAGCAGACTTCAAGTCGATATTTTGAATAAGGCTTACAGCAAGGGT 240 −1.152073379 −1 Stayer GGTGTGTAGGCACAGGGGTTGGATCTCTTCGATTTTTATGGGTATCTCACTCTACAATTT 241 1.252054372 1 Sprinter ACATGCTCAGAAATAAAAACATTAATTTTCGACAAATACTGTAGGATTTCAAGGGAAGAA 242 −1.171653431 −1 Stayer TTAAAGCTATAGTGAATGAAGCAATATATCGAGTTGTCTTCTAAAAGACAGTCTAATAAT 243 −1.176939591 −1 Stayer GAGTCTCTAGGTACCTGTCCGCTTCAGGTCGAGCTGTCAAGGGGCAAAAAAAAAAAAAAA 244 −1.229548609 −1 Stayer AGGGCACTGCCCTTGATCAGGTAAATGTTCGACCTGAAGCGGACAGGTACCTAGAGACTC 245 −1.145576167 −1 Stayer GAGTCTCTAGGTACCTGTCCGCTTCAGGTCGATGGTCGGCACATTTTCGTAGCCACCCTG 246 −1.282505466 −1 Stayer GAGTCTCTAGGTACCTGTCCGCTTCAGGTCGAAATTAACAGACACATCTGTGTCTGCTCT 247 −1.257983837 −1 Stayer GCGAGGTCATGAATGTACAAGTATAATGTCGAGTATAAGTTAAACGTGATTAAATGTAAG 248 −1.259633485 −1 Stayer GCGAGGTCATGAATGTACAAGTATAATGTCGATTAAAATATTTTACTTTTCCTTAATTAC 249 1.263289306 1 Sprinter ATGGGTATTGCTITATGCCTGCTGTGTTTCGAATTGAATGGAGACGCCTTTTGGTAGGAT 250 −1.144092755 −1 Stayer CTTACATTTAATCACGTTTAACTTATACTCGAGGTGCTCATCCCGAGGTACTTAGCGCCT 251 1.218623588 1 Sprinter ATCCTACCAAAAGGCGTCTCCATTCAATTCGATTAAAATATTTTACTTTTCCTTAATTAC 252 −1.523013774 −1 Stayer CAACGACACAAAGGTGTACACACAAACATCGATTTTTGCTAAGATGGTTGCAAATGATAG 253 −1.488754532 −1 Stayer CAACGACACAAAGGTGTACACACAAACATCGAAAGAAAGATTTCTTTAGACTCTTAAGAT 254 −1.352418666 −1 Stayer CAGCTGTACATTTTTAGTTGTGCGCACTTCGACGAGTCAAAACCGACGGAAGTCAGGCAG 255 −1.368213286 −1 Stayer AATCTCACTAGAAGGTACAGGTGTCAAGTCGACGAGTCAAAACCGACGGAAGTCAGGCAG 256 −1.166429544 −1 Stayer CTCAGGTTAAGTCCCCCTGTACCTGCTGTCGAGACAGACGTGTGCCTTCTTGAAAAAGCC

TABLE 33.d5 Probe Location 4 kb Sequence Location N Chr Start1 End1 Start2 End2 Chr Start1 End1 Start2 193 17 48760895 48760926 48985578 48985609 17 48756925 48760926 48985578 194 9 81548175 81548206 81579682 81579713 9 81544205 81548206 81579682 195 9 81540380 81540411 81579682 81579713 9 81540380 81544381 81579682 196 31 2794971 2795002 2851292 2851323 31 2791001 2795002 2851292 197 24 16803396 16803427 16918062 16918093 24 16803396 16807397 16914092 198 8 3352241 3352272 3404723 3404754 8 3352241 3356242 3404723 199 8 3439495 3439526 3479117 3479148 8 3435525 3439526 3475147 200 8 3439495 3439526 3469888 3469919 8 3435525 3439526 3469888 201 13 19588585 19588616 19619059 19619090 13 19584615 19588616 19615089 202 14 2229196 2229227 2274036 2274067 14 2229196 2233197 2274036 203 14 2229196 2229227 2401910 2401941 14 2229196 2233197 2401910 204 15 37903511 37903542 38029907 38029938 15 37903511 37907512 38029907 205 15 37903511 37903542 38069969 38070000 15 37903511 37907512 38069969 206 5 1010267 1010298 1038449 1038480 5 1006297 1010298 1034479 207 10 19508221 19508252 19593723 19593754 10 19508221 19512222 19589753 208 1 104992073 104992104 105164945 105164976 1 104992073 104996074 105160975 209 17 4337612 4337643 4528348 4528379 17 4333642 4337643 4524378 210 17 4418766 4418797 4517894 4517925 17 4414796 4418797 4513924 211 17 4418766 4418797 4528348 4528379 17 4414796 4418797 4524378 212 7 12601995 12602026 12717637 12717668 7 12601995 12605996 12713667 213 7 12717637 12717668 12737470 12737501 7 12713667 12717668 12737470 214 12 19894956 19894987 19974797 19974828 12 19894956 19898957 19970827 215 12 19992086 19992117 20053517 20053548 12 19992086 19996087 20049547 216 11 31942510 31942541 32032038 32032069 11 31942510 31946511 32032038 217 11 31953015 31953046 32042190 32042221 11 31953015 31957016 32038220 218 11 31953015 31953046 32032038 32032069 11 31953015 31957016 32032038 219 18 66450044 66450075 66500458 66500489 18 66446074 66450075 66496488 220 2 39767816 39767847 39804925 39804956 2 39763846 39767847 39804925 221 2 39767816 39767847 39839229 39839260 2 39763846 39767847 39835259 222 2 39767816 39767847 39835824 39835855 2 39763846 39767847 39835824 223 8 6868138 6868169 6923181 6923212 8 6868138 6872139 6923181 224 10 20037236 20037267 20084055 20084086 10 20037236 20041237 20080085 225 11 52882980 52883011 52915290 52915321 11 52882980 52886981 52911320 226 6 1098854 1098885 989242 989273 6 1098854 1102855 989242 227 11 17193641 17193672 17368932 17368963 11 17193641 17197642 17364962 228 11 17206623 17206654 17368932 17368963 11 17206623 17210624 17364962 229 11 17246461 17246492 17368932 17368963 11 17246461 17250462 17364962 230 11 17257199 17257230 17368932 17368963 11 17257199 17261200 17364962 231 11 17267739 17267770 17368932 17368963 11 17267739 17271740 17364962 232 11 17290815 17290846 17368932 17368963 11 17290815 17294816 17364962 233 1 61323595 61323626 61392274 61392305 1 61319625 61323626 61388304 234 1 61338770 61338801 61392274 61392305 1 61334800 61338801 61388304 235 1 61350438 61350469 61392274 61392305 1 61350438 61354439 61388304 236 1 109635329 109635360 109741316 109741347 1 109635329 109639330 109737346 237 1 109711483 109711514 109741316 109741347 1 109711483 109715484 109737346 238 1 109741316 109741347 109779877 109779908 1 109737346 109741347 109779877 239 25 25721432 25721463 25884535 25884566 25 25717462 25721463 25884535 240 11 22765246 22765277 22824653 22824684 11 22761276 22765277 22824653 241 23 34300375 34300406 34541066 34541097 23 34300375 34304376 34537096 242 23 34370479 34370510 34413070 34413101 23 34366509 34370510 34413070 243 2 39707018 39707049 39767816 39767847 2 39707018 39711019 39763846 244 2 39718640 39718671 39767816 39767847 2 39714670 39718671 39763846 245 2 39714609 39714640 39767816 39767847 2 39714609 39718610 39763846 246 2 39741527 39741558 39767816 39767847 2 39741527 39745528 39763846 247 2 66195314 66195345 66310948 66310979 2 66191344 66195345 66306978 248 2 66195314 66195345 66291709 66291740 2 66191344 66195345 66291709 249 2 66222272 66222303 66454370 66454401 2 66218302 66222303 66450400 250 2 66310948 66310979 66324859 66324890 2 66306978 66310979 66324859 251 2 66291709 66291740 66454370 66454401 2 66291709 66295710 66450400 252 16 35687870 35687901 35711378 35711409 16 35683900 35687901 35707408 253 16 35687870 35687901 35734783 35734814 16 35683900 35687901 35730813 254 11 25089999 25090030 25214955 25214986 11 25089999 25094000 25214955 255 11 25177016 25177047 25214955 25214986 11 25177016 25181017 25214955 256 21 5606382 5606413 5698848 5698879 21 5606382 5610383 5694878

TABLE 33.d6 4 kb Sequence Location N End2 Probe Primer ID-1 193 48989579 LMO7_17_48756745_48760926_48985578_48994371_FR OBD RD043.769 194 81583683 LY6D_9_81540380_81548206_81579682_81590550_FR OBD RD043.773 195 81583683 LY6D_9_81540380_81548206_81579682_81590550_RR OBD RD043.777 196 2855293 MAP3K4_31_2786762_2795002_2851292_2856203_FR OBD RD043.781 197 16918093 MAP3K9_24_16803396_16807626_16910389_16918093_RF OBD RD043.785 198 3408724 MAPK1_8_3352241_3355955_3404723_3412822_RR OBD RD043.789 199 3479148 MAPK1_8_3435741_3439526_3469888_3479148_FF OBD RD043.793 200 3473889 MAPK1_8_3435741_3439526_3469888_3479148_FR OBD RD043.797 201 19619090 MAPK3_13_19583177_19588616_19608792_19619090_FF OBD RD043.801 202 2278037 MAPK9_14_2229196_2237168_2274036_2279957_RR OBD RD043.805 203 2405911 MAPK9_14_2229196_2237168_2401910_2410518_RR OBD RD043.809 204 38033908 MDH1_15_37903511_37909683_38029907_38037711_RR OBD RD043.813 205 38073970 MDH1_15_37903511_37909683_38069969_38081007_RR OBD RD043.817 206 1038480 MDM4_5_1002213_1010298_1034976_1038480_FF OBD RD043.821 207 19593754 MED25_10_19508221_19515457_19591613_19593754_RF OBD RD043.825 208 105164976 MEF2A_1_104992073_105002150_105161756_105164976_RF OBD RD043.829 209 4528379 MIPEP_17_4332285_4337643_4521242_4528379_FF OBD RD043.833 210 4517925 MIPEP_17_4413535_4418797_4506914_4517925_FF OBD RD043.837 211 4528379 MIPEP_17_4413535_4418797_4521242_4528379_FF OBD RD043.841 212 12717668 MMP1_7_12601995_12610418_12711728_12717668_RF OBD RD043.845 213 12741471 MMP1_7_12711728_12717668_12737470_12745025_FR OBD RD043.849 214 19974828 MS4A2_12_19894956_19896244_19962410_19974828_RF OBD RD043.853 215 20053548 MS4A2_12_19992086_20002065_20049543_20053548_RF OBD RD043.857 216 32036039 MSI2_11_31942510_31947907_32032038_32042221_RR OBD RD043.861 217 32042221 MSI2_11_31953015_31955643_32032038_32042221_RF OBD RD043.865 218 32036039 MSI2_11_31953015_31955643_32032038_32042221_RR OBD RD043.869 219 66500489 MSTN_18_66448734_66450075_66490497_66500489_FF OBD RD043.873 220 39808926 MTHFR_2_39760745_39767847_39804925_39808549_FR OBD RD043.877 221 39839260 MTHFR_2_39760745_39767847_39835824_39839260_FF OBD RD043.881 222 39839825 MTHFR_2_39760745_39767847_39835824_39839260_FR OBD RD043.885 223 6927182 MTMR3_8_6868138_6874813_6923181_6926871_RR OBD RD043.889 224 20084086 MYBPC2_10_20037236_20038811_20080873_20084086_RF OBD RD043.893 225 52915321 MYH1_11_52882980_52886797_52907287_52915321_RF OBD RD043.897 226 993243 MYL1_6_1098854_1104299_989242_996235_RR OBD RD043.901 227 17368963 MYL4_11_17193641_17194702_17358881_17368963_RF OBD RD043.905 228 17368963 MYL4_11_17206623_17211708_17358881_17368963_RF OBD RD043.909 229 17368963 MYL4_11_17246461_17251113_17358881_17368963_RF OBD RD043.913 230 17368963 MYL4_11_17257199_17259878_17358881_17368963_RF OBD RD043.917 231 17368963 MYL4_11_17267739_17271299_17358881_17368963_RF OBD RD043.921 232 17368963 MYL4_11_17290815_17294484_17358881_17368963_RF OBD RD043.925 233 61392305 MYOZ1_1_61314759_61323626_61385709_61392305_FF OBD RD043.929 234 61392305 MYOZ1_1_61323626_61338801_61385709_61392305_FF OBD RD043.933 235 61392305 MYOZ1_1_61350438_61357018_61385709_61392305_RF OBD RD043.937 236 109741347 NDN_1_109635329_109640204_109733366_109741347_RF OBD RD043.941 237 109741347 NDN_1_109711483_109720818_109733366_109741347_RF OBD RD043.945 238 109783878 NDN_1_109733366_109741347_109779877_109789352_FR OBD RD043.949 239 25888536 NDUFA8_25_25717207_25721463_25884535_25891335_FR OBD RD043.953 240 22828654 NEUROD2_11_22762666_22765277_22824653_22836914_FR OBD RD043.957 241 34541097 NFIB_23_34300375_34312881_34537544_34541097_RF OBD RD043.961 242 34417071 NFIB_23_34364872_34370510_34413070_34423547_FR OBD RD043.965 243 39767847 NPPA_2_39707018_39708108_39760745_39767847_RF OBD RD043.969 244 39767847 NPPA_2_39714609_39718671_39760745_39767847_FF OBD RD043.973 245 39767847 NPPA_2_39714609_39718671_39760745_39767847_RF OBD RD043.977 246 39767847 NPPA_2_39741527_39742701_39760745_39767847_RF OBD RD043.981 247 66310979 PALLD_2_66194319_66195345_66291709_66310979_FF OBD RD043.985 248 66295710 PALLD_2_66194319_66195345_66291709_66310979_FR OBD RD043.989 249 66454401 PALLD_2_66212034_66222303_66449615_66454401_FF OBD RD043.993 250 66328860 PALLD_2_66291709_66310979_66324859_66327343_FR OBD RD043.997 251 66454401 PALLD_2_66291709_66310979_66449615_66454401_RF OBD RD043.1001 252 35711409 PCBP4_16_35681721_35687901_35707118_35711409_FF OBD RD043.1005 253 35734814 PCBP4_16_35681721_35687901_35729420_35734814_FF OBD RD043.1009 254 25218956 PHOSPHO1_11_25089999_25092180_25214955_25221072_RR OBD RD043.1013 255 25218956 PHOSPHO1_11_25177016_25183355_25214955_25221072_RR OBD RD043.1017 256 5698879 PIK3Rl_21_5606382_5618174_5697527_5698879_RF OBD RD043.1021

TABLE 33.d7 N Primer Sequence Primer ID-2 Primer Sequence 193 TTTTGTGTCCTAATGGAAGGCTGTGC OBD RD043.771 CCCGAGTGCTCAGATTCTTGCTGG 194 GGCACTTCTGGTGTTTCAGCCTC OBD RD043.775 CGGACGCTGGTTCCATAGTCGTG 195 CAGTGCGGTATCGGTGAAGGGAA OBD RD043.779 CGGACGCTGGTTCCATAGTCGTG 196 CCTGCCACATCCGCTCTTGGTTG OBD RD043.783 ACGAGCATTTATTGGGCACGGGC 197 CGTCTCCCCATTGTAAGGTAAACTCC OBD RD043.787 TGAAAGCAAAGCACTTGGAAAGCATA 198 GTTGTGTGGAAACCTCTTCTGCCCCA OBD RD043.791 GTAGATTTTGGACCTCGTGTCTCAGA 199 TGGTGTTGTGTGGAAACCTCTTCTGC OBD RD043.795 ATGTGGCTATCCAACTATCCCAGCAC 200 CCCTTTTCATCAATGTTCGGGTG OBD RD043.799 CCTGGGCGTCCTCAGACTGTCCG 201 CCGTGCCTTGGTTCTCTCTTCTG OBD RD043.803 GCGGTGTTGTGGGCATCAAGGTG 202 GGCTGACTGAAGATACTTTGGCAT OBD RD043.807 TTTTATCCTTGAAGCGTATTGAAT 203 CCTGGCTGACTGAAGATACTTTGGCA OBD RD043.811 TAAGAGTTGGGAAGTGGTCAAGC 204 TACCCATAAATGTGTTTGCTGTTCAC OBD RD043.815 CGGCAAGGGAGTAAACATCAGAGCAA 205 TACCCATAAATGTGTTTGCTGTTCAC OBD RD043.819 CCCTTTGTCTCCTGAGCATCTGGTTT 206 GACACTTGGAGCCTGTTGTTTCT OBD RD043.823 ACTCACATCAGTCAGCAGGAAGG 207 GAGTTGTAGTCCCCTGCCCACCT OBD RD043.827 CGTGTATTCTGCTGTTTCCAGGTGG 208 CACCACGCAGCAGCCCGAAACAT OBD RD043.831 GGGCAAGGAAACAGAGCCGTGTA 209 GGGAACTAACCCCACGACAAGAC OBD RD043.835 GAGTCTCCCAGTCTCAGCCCATC 210 GACTCCCACGGATAAGATGCTCC OBD RD043.839 GAGTCTCCCAGTCTCAGCCCATC 211 GGGAACTAACCCCACGACAAGAC OBD RD043.843 GGCTCAGGGTTAGGTCAGGAGTC 212 GGATTTCCTATGGCAGCCTCCTTGGA OBD RD043.847 CCCTTCTAACCACACACAAGTCCTTT 213 GGATTTCCTATGGCAGCCTCCTTGGA OBD RD043.851 TACATTCAGGAGGACTGGAGACG 214 GCTTTCCCTATTTGATTTCAGAAG OBD RD043.855 TAGGCAGGAACACTGTCTACTACA 215 GGGCTGTAACTGACCAGAATCTTTGA OBD RD043.859 TTACACCCTTCGGAGGCACTGGAACA 216 CAAGGGTGGTGTGACAGGAAGTC OBD RD043.863 GCGAGCCATCGGGAAAGAGCATC 217 TCAAGTCAGTGCCAGTCAAGGGC OBD RD043.867 CTCCCCACCCAAGCCAAACAGGT 218 CTTTGTGGTTCATCCTCAGCCCC OBD RD043.871 CTCCCCACCCAAGCCAAACAGGT 219 GGATAGTCTGTGGCAGGCTGGCTTTT OBD RD043.875 TTCTCTGCTCCTTCCTTTCCAAACTG 220 TGGCTACGGCTGTGAGAGATGGA OBD RD043.879 AGAGGAGGAAATGGCAGGCAGCC 221 TCACCCAAACCGTAGAGACAGGAGTG OBD RD043.883 TATCCCTAAATGTCCCTTTTCACAGC 222 GTGGCTACGGCTGTGAGAGATGG OBD RD043.887 CCTGCGTTTCTCCAAGGATGGTC 223 GGAACACCAATAAGTGGGCTAATACA OBD RD043.891 CCCTGTGGCAAGTGATGGCAGTAGAA 224 GGGCAGAGAAAAGAGTCACTGTG OBD RD043.895 TTCTGTGGTCCCTCCGCCTCCGC 225 CAGGGACTCCAGAATAACTGACCC OBD RD043.899 GCAGTTCAACAGCCTGGAGCAGC 226 CTCAAACACTCCCAGCGTTGGCA OBD RD043.903 GCCCTAACCTCTCCCCTTCACCA 227 GACTGTAAAGATGAAAGAAGATTC OBD RD043.907 AGAAGAGACTTACTGTGCTATTTT 228 CAAAAGTCTGCCAAGTTATTCCTGGG OBD RD043.911 TCAGACTCTAACCCACCTGTTCTTGG 229 GACTGTAAAGATGAAAGAAGATTC OBD RD043.915 CTTGGTTTCCTTTGCCTTCCAGAA 230 CAAAAGTCTGCCAAGTTATTCCTGGG OBD RD043.919 GGCTCTCACTCTTTCTCCTCAGCAGA 231 CAAAAGTCTGCCAAGTTATTCCTGGG OBD RD043.923 GGCAGGATGGCATTCCACCTTATGTC 232 GACTGTAAAGATGAAAGAAGATTC OBD RD043.927 GGTTGCTGTGACAAAATGCCATAG 233 GCTATTGTAAAGAGGCTATGCCAACT OBD RD043.931 CATTCAACATACCCTCCTCCTCGCTG 234 CCATTCAACATACCCTCCTCCTCGC OBD RD043.935 GGACATTATTCTCCAGGAAAGACCT 235 CATAAAGTAGAGGAGGACTGGTC OBD RD043.939 TCCCATTCAACATACCCTCCTCC 236 GCCCTCTTGGGACTGAACTCTCT OBD RD043.943 CGCCCCAACCTTGCTGGACATTG 237 CAGCCCTCTTGGGACTGAACTCTCTA OBD RD043.947 CAGAAGAACTCCTGAAACGCCAAGAA 238 CAGCCCTCTTGGGACTGAACTCTCTA OBD RD043.951 GCCAACACTGTGGAACTGAATCTAAG 239 TCATAGGCAATAGATTTCCTGGGAGC OBD RD043.955 CAGCCGACAGTAGCCCTTAGATTGCT 240 GACAGCCAGACTGATGGGTGAGG OBD RD043.959 CCACTCCCTTCCCATTCCTCCTT 241 CACTCGGCAGATGGCGTGGCATA OBD RD043.963 TCTCTGCCCGTGACTTTGCTCCT 242 ATGTAACTGCCTACGAACCCTCCAGG OBD RD043.967 AGATTAGGGTTGCTGAGTGGGTCAAT 243 GTGGCTACGGCTGTGAGAGATGG OBD RD043.971 CAGGAACCTCTAATCCACGCCCT 244 TGGCTACGGCTGTGAGAGATGGA OBD RD043.975 TTCCAGGACAACCGCATCCAGGG 245 GACCACCCCGCCCAGGCTGACCT OBD RD043.979 ACGGCTGTGAGAGATGGAGAGTC 246 TGGCTACGGCTGTGAGAGATGGA OBD RD043.983 AGGTGGCTTCCTGTGGGCTGAGA 247 GAGGAAGATTGGCAACAGATGCTA OBD RD043.987 CCTCTATGTTTTCTCGTTCTTTTA 248 CCCACACACCACACCACTCATCA OBD RD043.991 AGGCAGTCCACAAAGCCAGCGTG 249 GGCTTCTGGCACTTACTGAATGGCTT OBD RD043.995 AGGTGGAAATGTAAGGCTGAGTAGGC 250 GAAAGAGAAATACACTCAACAGAGA OBD RD043.999 TCCTCTATGTTTTCTCGTTCTTTTA 251 TCCAGAGGGCTGAAGACTTGAGAAAG OBD RD043.1003 GGGACTCATAGGGAGACACATTA 252 TAGGTCCTTGGCATACGCATTGA OBD RD043.1007 CTAAATAAAAGAGCACTACTGCCAGA 253 GAGTCTACGCTACAGATACAAGGG OBD RD043.1011 AGAATCCACAAATCCATACTGATA 254 ATGGTCTGTGCCCCTGGTGCCTA OBD RD043.1015 ATTGGGCAGGAGGTGAGGAACTG 255 CACCTCACATTCTAACATCTCAGTCT OBD RD043.1019 TTGATGCTCTGGATTGGGCAGGAGGT 256 CCAGACAGGAGGAGAGAACAGATTTC OBD RD043.1023 GTTTTGTTCCCAAGTGCCTCTGACAG

TABLE 33.d8 N Probe Marker 193 LMO7 OBD RD043.769.771 194 LY6D OBD RD043.773.775 195 LY6D OBD RD043.777.779 196 MAP3K4 OBD RD043.781.783 197 MAP3K9 OBD RD043.785.787 198 MAPK1 OBD RD043.789.791 199 MAPK1 OBD RD043.793.795 200 MAPK1 OBD RD043.797.799 201 MAPK3 OBD RD043.801.803 202 MAPK9 OBD RD043.805.807 203 MAPK9 OBD RD043.809.811 204 MDH1 OBD RD043.813.815 205 MDH1 OBD RD043.817.819 206 MDM4 OBD RD043.821.823 207 MED25 OBD RD043.825.827 208 MEF2A OBD RD043.829.831 209 MIPEP OBD RD043.833.835 210 MIPEP OBD RD043.837.839 211 MIPEP OBD RD043.841.843 212 MMP1 OBD RD043.845.847 213 MMP1 OBD RD043.849.851 214 MS4A2 OBD RD043.853.855 215 MS4A2 OBD RD043.857.859 216 MSI2 OBD RD043.861.863 217 MSI2 OBD RD043.865.867 218 MSI2 OBD RD043.869.871 219 MSTN OBD RD043.873.875 220 MTHFR OBD RD043.877.879 221 MTHFR OBD RD043.881.883 222 MTHFR OBD RD043.885.887 223 MTMR3 OBD RD043.889.891 224 MYBPC2 OBD RD043.893.895 225 MYH1 OBD RD043.897.899 226 MYL1 OBD RD043.901.903 227 MYL4 OBD RD043.905.907 228 MYL4 OBD RD043.909.911 229 MYL4 OBD RD043.913.915 230 MYL4 OBD RD043.917.919 231 MYL4 OBD RD043.921.923 232 MYL4 OBD RD043.925.927 233 MYOZ1 OBD RD043.929.931 234 MYOZ1 OBD RD043.933.935 235 MYOZ1 OBD RD043.937.939 236 NDN OBD RD043.941.943 237 NDN OBD RD043.945.947 238 NDN OBD RD043.949.951 239 NDUFA8 OBD RD043.953.955 240 NEUROD2 OBD RD043.957.959 241 NFIB OBD RD043.961.963 242 NFIB OBD RD043.965.967 243 NPPA OBD RD043.969.971 244 NPPA OBD RD043.973.975 245 NPPA OBD RD043.977.979 246 NPPA OBD RD043.981.983 247 PALLD OBD RD043.985.987 248 PALLD OBD RD043.989.991 249 PALLD OBD RD043.993.995 250 PALLD OBD RD043.997.999 251 PALLD OBD RD043.1001.1003 252 PCBP4 OBD RD043.1005.1007 253 PCBP4 OBD RD043.1009.1011 254 PHOSPHO1 OBD RD043.1013.1015 255 PHOSPHO1 OBD RD043.1017.1019 256 PIK3R1 OBD RD043.1021.1023

TABLE 33.e1 N Probe GeneLocus Probe_Count_Total Probe_Count_Sig 257 PLXDC1_11_23117935_23125158_23188757_23196195_RR PLXDC1 1 27 258 PRKAG2_4_103028895_103043216_103233754_103234780_RF PRKAG2 2 177 259 PRKAG2_4_103028895_103043216_103342192_103345172_RR PRKAG2 2 177 260 PRKCA_11_13786370_13794644_13849517_13854647_RF PRKCA 1 60 261 PRKCB_13_23475428_23483033_23690253_23695272_RF PRKCB 2 19 262 PRKCB_13_23532412_23540462_23690253_23695272_RF PRKCB 2 19 263 RAB33B_2_91817483_91819013_91968018_91981648_FF RAB33B 2 45 264 RAB33B_2_91817483_91819013_91968018_91981648_RR RAB33B 2 45 265 RAG2_12_2995445_3004477_3070874_3072970_RF RAG2 3 49 266 RAG2_12_2995445_3004477_3070874_3072970_RR RAG2 3 49 267 RAG2_12_2995445_3004477_3124836_3128121_RF RAG2 3 49 268 RASSF5_5_2727413_2732312_2768970_2779500_FF RASSF5 3 31 269 RASSF5_5_2727413_2732312_2857276_2865680_FF RASSF5 3 31 270 RASSF5_5_2752106_2755183_2768970_2779500_FF RASSF5 3 31 271 RBPJL_22_34286715_34290143_34327562_34334894_FR RBPJL 2 28 272 RBPJL_22_34286715_34290143_34327562_34334894_RR RBPJL 2 28 273 SCN10A_16_46394076_46405616_46559136_46563398_RF SCN10A 3 120 274 SCN10A_16_46394076_46405616_46644599_46646012_RF SCN10A 3 120 275 SCN10A_16_46542432_46554053_46644599_46646012_RF SCN10A 3 120 276 SCN2B_7_25981242_25985420_26023779_26030228_FF SCN2B 2 31 277 SCN2B_7_25981242_25985420_26102356_26109968_FF SCN2B 2 31 278 SCN4B_7_25954012_25959734_25981242_25985420_RF SCN4B 1 31 279 SCN5A_16_46559136_46563398_46724067_46732988_FF SCN5A 2 30 280 SCN5A_16_46559136_46563398_46724067_46732988_FR SCN5A 2 30 281 SELL_5_6104471_6117065_6186372_6188629_FR SELL 1 111 282 SEPT7_4_65366992_65373527_65534812_65540822_RF SEPT7 1 127 283 SGCA_11_25806231_25808754_26000893_26002740_RF SGCA 2 13 284 SGCA_11_25806231_25808754_26000893_26002740_RR SGCA 2 13 285 SIK2_7_20268830_20278159_20296076_20300289_FR SIK2 4 204 286 SIK2_7_20268830_20278159_20375473_20380173_FF SIK2 4 204 287 SIK2_7_20268830_20278159_20391427_20402715_FR SIK2 4 204 288 SIK2_7_20268830_20278159_20407650_20411122_FR SIK2 4 204 289 SNAP29_8_3045435_3054804_3164300_3172603_FF SNAP29 2 50 290 SNAP29_8_3117316_3123446_3164300_3172603_FF SNAP29 2 50 291 SPRED1_1_149873033_149876737_150087432_150097168_RF SPRED1 8 166 292 SPRED1_1_149873033_149876737_150099832_150110035_RF SPRED1 8 166 293 SPRED1_1_149910043_149913663_150087432_150097168_RF SPRED1 8 166 294 SPRED1_1_149910043_149913663_150099832_150110035_RF SPRED1 8 166 295 SPRED1_1_149923380_149924915_150099832_150110035_RF SPRED1 8 166 296 SPRED1_1_150016977_150019540_150099832_150110035_RF SPRED1 8 166 297 SPRED1_1_150032266_150036031_150087432_150097168_RF SPRED1 8 166 298 SPRED1_1_150068252_150074099_150099832_150110035_RF SPRED1 8 166 299 SRC_22_27681702_27686300_27826003_27831147_FR SRC 1 28 300 SRF_20_42097551_42100241_42177997_42186255_FR SRF 1 31 301 STAT1_18_67266270_67281181_67315145_67320245_RF STAT1 3 37 302 STAT1_18_67266270_67281181_67340514_67345500_RF STAT1 3 37 303 STAT1_18_67266270_67281181_67404406_67407824_RR STAT1 3 37 304 STAT3_11_20601546_20610244_20625038_20630547_FF STAT3 2 28 305 STAT3_11_20601546_20610244_20625038_20630547_RF STAT3 2 28 306 STAT5A_11_20625038_20630547_20748936_20755885_FF STAT5A 1 30 307 STXBP4_11_29798087_29803880_29820062_29826392_RF STXBP4 2 58 308 STXBP4_11_29820062_29826392_29856303_29862822_FR STXBP4 2 58 309 TGFBR1_25_5777848_5781338_5953575_5963779_RF TGFBR1 2 29 310 TGFBR1_25_5838527_5844153_5953575_5963779_RF TGFBR1 2 29 311 TMEM156_3_88174369_88185533_88338789_88351273_FF TMEM156 1 90 312 TOB1_11_26381091_26387145_26421158_26424834_RR TOB1 2 31 313 TOB1_11_26381091_26387145_26552180_26554959_RR TOB1 2 31 314 TSPAN3_1_117377450_117387477_117527452_117533304_RF TSPAN3 2 53 315 TSPAN3_1_117501086_117515708_117527452_117533304_RF TSPAN3 2 53 316 TSPAN5_3_40723323_40732311_40838443_40842795_RF TSPAN5 1 176 317 VAV1_7_4248599_4253460_4432636_4444354_FF VAV1 1 38 318 VEGFC_27_31943096_31950700_31994751_32003367_RR VEGFC 2 54 319 VEGFC_27_31943096_31950700_32006848_32015827_RR VEGFC 2 54 320 ZFHX3_3_20954370_20958861_21248124_21260027_FF ZFHX3 1 141

TABLE 33.e2 N HyperG_Stats FDR_HyperG Percent_Sig logFC AveExpr 257 0.178891485 0.267074007 3.7 −0.498546573 8.334899675 258 0.248623084 0.310300562 1.13 −0.938829032 8.830030136 259 0.248623084 0.310300562 1.13 −0.409357346 9.945611435 260 0.303088108 0.331342084 1.67 −0.32685719 9.445425416 261 0.009980432 0.049518297 10.53 −0.470343416 9.5078615 262 0.009980432 0.049518297 10.53 −0.310412046 10.44482443 263 0.046697041 0.122937109 4.44 −0.192180899 10.74179204 264 0.046697041 0.122937109 4.44 −0.354237277 9.242623502 265 0.006920652 0.037512367 6.12 0.358172408 9.004366375 266 0.006920652 0.037512367 6.12 0.207569755 9.114059545 267 0.006920652 0.037512367 6.12 0.274277591 8.211642632 268 0.001955877 0.014841655 9.68 −0.380422279 10.05354755 269 0.001955877 0.014841655 9.68 −0.379141769 10.15172147 270 0.001955877 0.014841655 9.68 −0.321187765 8.346983577 271 0.020494302 0.075554863 7.14 −0.418632216 9.712363657 272 0.020494302 0.075554863 7.14 0.256227174 9.629544001 273 0.059031661 0.137915817 2.5 −0.303249497 9.538210055 274 0.059031661 0.137915817 2.5 −0.392996971 10.12637726 275 0.059031661 0.137915817 2.5 −0.517204321 9.549017556 276 0.024599258 0.075554863 6.45 −0.330982641 8.754115738 277 0.024599258 0.075554863 6.45 −0.600780426 8.122591447 278 0.198752749 0.267074007 3.23 −0.513873909 8.171494225 279 0.023201487 0.075554863 6.67 −0.275782912 9.599314892 280 0.023201487 0.075554863 6.67 −0.332593132 9.221879302 281 0.368532709 0.369972517 0.9 −0.192237265 11.73871812 282 0.369595168 0.369972517 0.79 0.236701745 11.5277415 283 0.004781729 0.029373479 15.38 −0.299567355 9.597332982 284 0.004781729 0.029373479 15.38 −0.395116377 8.436344868 285 0.060939547 0.137915817 1.96 −0.250370376 8.821107854 286 0.060939547 0.137915817 1.96 −0.205233587 8.887500946 287 0.060939547 0.137915817 1.96 −0.328539529 8.245361941 288 0.060939547 0.137915817 1.96 −0.366691703 8.419551683 289 0.055461917 0.137588217 4 −0.245937866 10.96109836 290 0.055461917 0.137588217 4 −0.261369209 11.03851689 291 0.0000634628527405492 0.001364451 4.82 0.626539336 8.460307208 292 0.0000634628527405492 0.001364451 4.82 0.45135055 7.830572417 293 0.0000634628527405492 0.001364451 4.82 0.514959643 8.178202101 294 0.0000634628527405492 0.001364451 4.82 0.330234467 7.825606038 295 0.0000634628527405492 0.001364451 4.82 0.347918733 8.022790865 296 0.0000634628527405492 0.001364451 4.82 0.265700639 8.225367878 297 0.0000634628527405492 0.001364451 4.82 0.418287098 8.296113768 298 0.0000634628527405492 0.001364451 4.82 0.292449794 7.689848783 299 0.183998999 0.267074007 3.57 −0.257211227 8.96771926 300 0.198752749 0.267074007 3.23 −0.289791551 11.53768831 301 0.003219239 0.020764093 8.11 0.950923864 8.127367441 302 0.003219239 0.020764093 8.11 0.339957139 10.88074422 303 0.003219239 0.020764093 8.11 0.422734986 8.738942644 304 0.020494302 0.075554863 7.14 −0.34818003 9.404675926 305 0.020494302 0.075554863 7.14 −0.308351369 10.09067586 306 0.193928419 0.267074007 3.33 −0.327160983 10.04088364 307 0.070089709 0.151221234 3.45 0.301994949 8.888178828 308 0.070089709 0.151221234 3.45 0.297112393 8.516631477 309 0.02183283 0.075554863 6.9 −0.462921799 9.298865314 310 0.02183283 0.075554863 6.9 −0.502142385 8.308741006 311 0.355201455 0.369972517 1.11 −0.25947705 8.734272977 312 0.024599258 0.075554863 6.45 −0.67235893 8.052267141 313 0.024599258 0.075554863 6.45 −0.658106699 8.007819166 314 0.060873696 0.137915817 3.77 −0.576817806 8.097751634 315 0.060873696 0.137915817 3.77 −0.568732319 8.537384311 316 0.341994894 0.367644511 0.57 −0.456101192 9.282066601 317 0.23001238 0.297307866 2.63 −0.183925655 10.27585426 318 0.062698978 0.139451175 3.7 −0.51992089 8.803285229 319 0.062698978 0.139451175 3.7 −0.570858041 8.216821116 320 0.365633172 0.369972517 0.71 −0.359210093 10.90927278

TABLE 33.e3 N t P.Value adj.P.Val B FC 257 −8.679819127 0.0000000466671136396821 0.000070018619349385 8.618875681 0.707819507 258 −12.72862254 0.0000000000880568203541454 0.000000960392461716811 14.05544918 0.521656113 259 −7.136605672 0.000000846145358915483 0.000471545 5.94886147 0.752958707 260 −7.042847832 0.00000101943002074247 0.00053024 5.774815448 0.797271393 261 −7.060938638 0.000000983342866158556 0.000518381 5.808503626 0.721792764 262 −6.523007013 0.00000292622869023077 0.001037747 4.785416246 0.806411408 263 −6.177861318 0.00000601133616970513 0.001701441 4.106203741 0.875281571 264 −6.685600302 0.00000209595044430101 0.000822758 5.09928145 0.782283111 265 5.396796706 0.0000323877534937054 0.005178058 2.508645352 1.281801096 266 5.003725624 0.0000775486565602272 0.00961269 1.677385244 1.154741363 267 6.369772263 0.00000402056197173788 0.001307018 4.48601267 1.209388354 268 −5.516753496 0.0000248906319064535 0.004416684 2.75901438 0.768212701 269 −5.382597738 0.0000334164554567416 0.005277635 2.478900424 0.768894855 270 −5.006426169 0.0000770809956858349 0.009606804 1.683147538 0.800410631 271 −5.662219604 0.0000181264479152015 0.003741337 3.060319651 0.748133575 272 5.012432569 0.0000760511136821973 0.009570174 1.695961392 1.194351241 273 −6.533997102 0.00000286064608645947 0.001033276 4.806755937 0.810424954 274 −6.783534136 0.00000171722954949946 0.00071265 5.286406035 0.761545969 275 −7.367545782 0.000000537461051340749 0.00033823 6.371766941 0.698724522 276 −5.071224906 0.0000666805443887129 0.008670693 1.821215505 0.794994816 277 −6.716956804 0.00000196610975254916 0.0007907 5.159353307 0.659397158 278 −6.486863965 0.00000315305553468220 0.001088502 4.715109769 0.700339367 279 −6.351012197 0.00000418091312232632 0.00133884 4.449120217 0.826001948 280 −6.052890375 0.00000783121810960962 0.002092437 3.856049162 0.794107853 281 −5.560217945 0.0000226347401909662 0.004245102 2.849313135 0.875247375 282 5.779181792 0.0000140717989649137 0.003153542 3.300663941 1.178295788 283 −7.386976626 0.000000517495203192340 0.000336458 6.406972586 0.812496017 284 −6.766116831 0.00000177901940080403 0.000730522 5.253232767 0.760428033 285 −7.016707493 0.00000107401014567895 0.000532857 5.726048608 0.840680564 286 −5.060793325 0.0000682529865421064 0.00878729 1.799014592 0.867398235 287 −5.72356327 0.0000158691029014987 0.003458401 3.186592403 0.79634223 288 −7.062768364 0.000000979767285195514 0.000518381 5.81190808 0.775558922 289 −5.519623473 0.0000247348136116668 0.004416684 2.764983829 0.843267427 290 −5.324822449 0.0000379586640410418 0.005899472 2.357637174 0.834295744 291 8.610941071 0.0000000527587433889362 0.000076226614059348 8.507428978 1.543857222 292 8.317816898 0.0000000895362606598224 0.000094400257522694 8.025208094 1.367319647 293 5.398124663 0.0000322932145065220 0.005178058 2.51142608 1.428954167 294 5.241619663 0.0000456337287914882 0.006692375 2.18236792 1.257217681 295 5.310396024 0.0000391882227946439 0.00599503 2.327300642 1.272723241 296 5.519453444 0.0000247440170633763 0.004416684 2.764630201 1.202219761 297 7.351175156 0.000000554901072898733 0.00033823 6.342060509 1.336339985 298 5.014061752 0.0000757741890045537 0.009566185 1.699436487 1.224718167 299 −6.350304057 0.00000418709338863960 0.00133884 4.447726623 0.836703731 300 −5.771975103 0.0000142923844781131 0.003153542 3.285905862 0.818020242 301 6.786415088 0.00000170722463564491 0.00071265 5.291888693 1.933110174 302 5.902616329 0.0000107912833479968 0.002598568 3.552375976 1.265718991 303 5.329665604 0.0000375547764940088 0.005860047 2.367816494 1.340466334 304 −5.50999994 0.0000252612746619697 0.00443021 2.744963363 0.785574481 305 −6.758325987 0.00000180739710817034 0.000734443 5.238379279 0.807564071 306 −6.387863787 0.00000387192196030923 0.001269275 4.521541626 0.797103527 307 7.516520233 0.000000402590246451762 0.000285546 6.640189451 1.232848009 308 6.214597334 0.00000556381172965962 0.001607736 4.179317957 1.228682697 309 −5.501989713 0.0000257082159965563 0.004477132 2.728290772 0.725515429 310 −5.432137617 0.0000299655620481664 0.004995541 2.58258052 0.706057515 311 −5.691989465 0.0000169925238007217 0.003622286 3.121658976 0.835390678 312 −8.960872932 0.0000000284628323441866 0.000048275438684640 9.066366288 0.627479865 313 −8.504782119 0.0000000638163252172577 0.000078597025797400 8.334275623 0.633709391 314 −9.911052133 0.00000000574350539340819 0.000013179655611580 10.49543486 0.670440958 315 −12.64601994 0.0000000000984765405503011 0.000000960392461716811 13.96387344 0.674208949 316 −7.115525574 0.000000882250643786341 0.000484741 5.909847949 0.728953558 317 −5.065028806 0.0000676100320214694 0.008756001 1.80802993 0.880304376 318 −6.932852329 0.00000127040040821895 0.00058998 5.568900951 0.697410075 319 −6.149465237 0.00000638253863761245 0.001778449 4.049556555 0.673216275 320 −10.65803034 0.00000000175481548070441 0.00000570461265852324 11.5327881 0.779591306

TABLE 33.e4 Loop Probe sequence N FC_1 LS Detected 60 mer 257 −1.412789547 −1 Stayer AGTATTTGTATTTATTCTGGGAGTTTCATCGAACTGGCTTCATGCCAGATGCTGGAATTG 258 −1.91697169 −1 Stayer AAGTTAGTACTGCATTGTTAGTCAAGTGTCGAAATTGCTATGTATACCAAAGATTAAGGC 259 −1.328094078 −1 Stayer GCCTTAATCTTTGGTATACATAGCAATTTCGACCCACACAGCTCAAGAAGCTAATGCGCA 260 −1.254278039 −1 Stayer GTACAATATAGAGACATCATTCTCGTTATCGATTGGCGCACAAGTGCCAGGGACACCTGC 261 −1.385439215 −1 Stayer GGAAGAGGAAAAGAGAACTTAAAGAAGATCGAGAGAAAAGAAGGACAGACGAGGCTTCCA 262 −1.240061822 −1 Stayer GGAAGAGGAAAAGAGAACTTAAAGAAGATCGACGGCAGCATAGCCTCTGAGCTGGACAGG 263 −1.142489494 −1 Stayer TACAGGTGCCGTGTACCACTTTGATAAGTCGAACATTTGTTATTTTTTGTCTTGGTAATT 264 −1.278309587 −1 Stayer AAAACTTTCATCGCAAATGTACTAGCTGTCGAAAACAGCACAGCTTTTTGAGCCAGAAAA 265 1.281801096 1 Sprinter GTGCTTCTTTAAGATACCAGATAATTGATCGATACGACAGAACCTAGAAAAAGTTCCGAG 266 1.154741363 1 Sprinter CTCGGAACTTTTTCTAGGTTCTGTCGTATCGATTCAATTCGTATATCTCCCTCTTTCTCA 267 1.209388354 1 Sprinter GGTCTACCCGTGCGTGTTAACGCCGGGGTCGATACGACAGAACCTAGAAAAAGTTCCGAG 268 −1.301722815 −1 Stayer CGGCAGAGCTCACTGCAGTCAATTGGAATCGAACACTATGATAATTCTTTCCCAGATTCA 269 −1.300567943 −1 Stayer CGGCAGAGCTCACTGCAGTCAATTGGAATCGAGTTTATGCCTATCATAGGACTTGAACAG 270 −1.249358718 −1 Stayer TCTTCATTTATTTAGTGCTCACAAAAACTCGAACACTATGATAATTCTTTCCCAGATTCA 271 −1.3366597 −1 Stayer GGGCGTATTGCTATGGTTATGCCCCAGCTCGATTGTCTTATTTTTATTTATTTCTATCAC 272 1.194351241 1 Sprinter CTTTTTTACAAATCCTAAAGGATGCCCCTCGATTGTCTTATTTTTATTTATTTCTATCAC 273 −1.233920543 −1 Stayer ACCAGTGTCATCAGTACCCTAGAGGGCTTCGATGTTGTCTGCCTTTTTAATTTTTAACCA 274 −1.313118369 −1 Stayer CCTTTGAGTCTCTGGTCAAGATTCTGGCTCGATGTTGTCTGCCTTTTTAATTTTTAACCA 275 −1.431179196 −1 Stayer CCTTTGAGTCTCTGGTCAAGATTCTGGCTCGAAGATTAGAAATATTTGGATATATTTCTA 276 −1.257869837 −1 Stayer GTGCGCTGCGCAGCTTAAACAGCAGAATTCGATGATTCTTGCCCGAGTCATATTTCACTA 277 −1.516536715 −1 Stayer GTGCGCTGCGCAGCTTAAACAGCAGAATTCGATCTTAAATTTATTGTATTTTGTTTGCAT 278 −1.427879178 −1 Stayer GTGCGCTGCGCAGCTTAAACAGCAGAATTCGACAAGGATCAGATATCATTAAGTCAAGTT 279 −1.210650898 −1 Stayer ACCAGTGTCATCAGTACCCTAGAGGGCTTCGAATGTTGAAACATACTCTCCAGTGTGATG 280 −1.25927479 −1 Stayer ACCAGTGTCATCAGTACCCTAGAGGGCTTCGAAACAAATGCTTTATATACTTACATCATC 281 −1.142534132 −1 Stayer AGTATTGGGAAGGAGTCACGGTCAGTAATCGAGAGCAGCATGTTAGCTCTCCGCCTTCGG 282 1.178295788 1 Sprinter CCCCTGCCTTACTCCCAGGGGCCGCCATTCGATGGGGGCACCGGGCAAGTCACTCACCCT 283 −1.230775265 −1 Stayer AAGGGGAAAAAATAAAAATAGAAGACCATCGAATCCGGTACTTTCTGGCCTTCCAAAAAG 284 −1.315048836 −1 Stayer CTTTTTGGAAGGCCAGAAAGTACCGGATTCGACCGTGGTGTATAATCCTTTTAATATACT 285 −1.189512454 −1 Stayer ATAAGTTTGTTCTGTAACCGTAATTAAGTCGAAGGATGTTGGTCCTAGACCCATCCAAAC 286 −1.152872993 −1 Stayer ATAAGTTTGTTCTGTAACCGTAATTAAGTCGAATAGCCCACGTTCAAGTGGAGAGGAATT 287 −1.255741517 −1 Stayer ATAAGTTTGTTCTGTAACCGTAATTAAGTCGACAAATTCTATCAACTGATGAATTTATAA 288 −1.289392684 −1 Stayer ATAAGTTTGTTCTGTAACCGTAATTAAGTCGAAGCTAAAAATATGCTTTAGTTTAAAATT 289 −1.185863426 −1 Stayer GCAAAGAAATATCTTTTATTTGCAAAATTCGAGATCTGGGGGTACTGGGTGGACTCTGGG 290 −1.198615727 −1 Stayer ACAAAGATTCTGTGGTTCCTTACCTTCTTCGAGATCTGGGGGTACTGGGTGGACTCTGGG 291 1.543857222 1 Sprinter GTTTGAAGTTTTGATTATTGCATGTAATTCGACTCTAGAAAAGTCTTTGAAAGATAAAAG 292 1.367319647 1 Sprinter TCAGTTATGGACATGTCTTGAAGTTAAATCGACTCTAGAAAAGTCTTTGAAAGATAAAAG 293 1.428954167 1 Sprinter GTTTGAAGTTTTGATTATTGCATGTAATTCGATCAAACATTATTCTGGATGTTTAAGTGA 294 1.257217681 1 Sprinter TCAGTTATGGACATGTCTTGAAGTTAAATCGATCAAACATTATTCTGGATGTTTAAGTGA 295 1.272723241 1 Sprinter TCAGTTATGGACATGTCTTGAAGTTAAATCGAATACACAGGGTGTGAGATTAAGAGAAGA 296 1.202219761 1 Sprinter TCAGTTATGGACATGTCTTGAAGTTAAATCGAGAAATGTGACGCAATAAATTTCCGTTGT 297 1.336339985 1 Sprinter GTTTGAAGTTTTGATTATTGCATGTAATTCGAAAGCCCAGGTTGTCACTGGGCTTCTGAC 298 1.224718167 1 Sprinter TCAGTTATGGACATGTCTTGAAGTTAAATCGAATATTACCTAAATTTTATCTATATAGAA 299 −1.195166178 −1 Stayer GGGAGCTAAAAGTACAATTTTTAAAGAGTCGATCCGTCACGTAGCAATATCAGCTGTGCG 300 −1.222463636 −1 Stayer TGCCAGTGTACCCAATAGGTACGGCCCGTCGAGTCACCCCAGTTCTGAGTCACCCCACTT 301 1.933110174 1 Sprinter AAAACCCAAGTAAATGTCCTTGATTATTTCGAGGGTTTTTTTTTTTTTTAATTGGTTTTA 302 1.265718991 1 Sprinter TAAAACCCAAAGACTTCAGCTTTCCCTCTCGAGGGTTTTTTTTTTTTTTAATTGGTTTTA 303 1.340466334 1 Sprinter TAAAACCAATTAAAAAAAAAAAAAACCCTCGAGTCTCTTAACCAATTACATGTGTGTTGG 304 −1.272953774 −1 Stayer ATGGCCCAATGGAATCAGCTGCAGCAGCTCGATGACCTGCACTAGGTACCGCAATGACCT 305 −1.238291841 −1 Stayer AGGTCATTGCGGTACCTAGTGCAGGTCATCGAGCCTGATTGTAATTTATAGACTGAACAG 306 −1.254542185 −1 Stayer AGGTCATTGCGGTACCTAGTGCAGGTCATCGAGCATGCGCTGCTTGAGCGTCCGCGGCAG 307 1.232848009 1 Sprinter ATTGCTTAAAAGTAAAAGTGCCATTGAGTCGAAAAACTTTTGAGGCATCCACTGAAAAGC 308 1.228682697 1 Sprinter ATTGCTTAAAAGTAAAAGTGCCATTGAGTCGAATATTAATGTTTTCCAACAACAGATTTA 309 −1.378330439 −1 Stayer AGCTGATTTTACTCTTGGATTTATTTCATCGACTGCGAACTCCGTGGAGCTCTAGAGAGA 310 −1.416315213 −1 Stayer AGCTGATTTTACTCTTGGATTTATTTCATCGACTAATAAAGTAGCATCAAAATATATAAG 311 −1.19704472 −1 Stayer GGTTCACAATGTAGCTATTTCCAAGCGATCGATTCAGTTCCACCTAAGTTCTTACTGATA 312 −1.593676636 −1 Stayer TCATCCATGGAATGTAATGACTATGAGATCGAATTAATACCTTTTGAAAAAAACTTAGCA 313 −1.578010384 −1 Stayer TCATCCATGGAATGTAATGACTATGAGATCGACTCTATGCTCCAGTCATTTAAAAATAGT 314 −1.491555651 −1 Stayer TAGTGACTTTCCCCAAAATAAAGTACATTCGATATTTGGCCAGATTTCCTGGCTAAAGTT 315 −1.483219708 −1 Stayer TAGTGACTTTCCCCAAAATAAAGTACATTCGAGATTTTCCTGACAAGGTACCACCCAAGC 316 −1.371829506 −1 Stayer ATATTTGTACTGGCAAACTGTTCTTTACTCGATACAGTCAGCTCCCTGTACACTCAGGAA 317 −1.135970725 −1 Stayer ATGGAGTACCTGAGAAGGTGATGTTAGCTCGAAAAAATATCTGCCAAGAGTGTGGTACTT 318 −1.433876619 −1 Stayer GCTCAATGAAAGGGTTCCAAATCATTGATCGATCACTGACACTGCTCACTGTGATCTCTT 319 −1.485406752 −1 Stayer GCTCAATGAAAGGGTTCCAAATCATTGATCGATTTGGACCTTGAGTGCGCAGTGTCTGTG 320 −1.282723386 −1 Stayer ATTATGATTGTGGCAATGCTTCGGAAGGTCGAAACCACCCTTTAAAAAAACATTTTTTTA

TABLE 33.e5 Probe Location 4 kb Sequence Location N Chr Start1 End1 Start2 End2 Chr Start1 End1 Start2 257 11 23117935 23117966 23188757 23188788 11 23117935 23121936 23188757 258 4 103028895 103028926 103234749 103234780 4 103028895 103032896 103230779 259 4 103028895 103028926 103342192 103342223 4 103028895 103032896 103342192 260 11 13786370 13786401 13854616 13854647 11 13786370 13790371 13850646 261 13 23475428 23475459 23695241 23695272 13 23475428 23479429 23691271 262 13 23532412 23532443 23695241 23695272 13 23532412 23536413 23691271 263 2 91818982 91819013 91981617 91981648 2 91815012 91819013 91977647 264 2 91817483 91817514 91968018 91968049 2 91817483 91821484 91968018 265 12 2995445 2995476 3072939 3072970 12 2995445 2999446 3068969 266 12 2995445 2995476 3070874 3070905 12 2995445 2999446 3070874 267 12 2995445 2995476 3128090 3128121 12 2995445 2999446 3124120 268 5 2732281 2732312 2779469 2779500 5 2728311 2732312 2775499 269 5 2732281 2732312 2865649 2865680 5 2728311 2732312 2861679 270 5 2755152 2755183 2779469 2779500 5 2751182 2755183 2775499 271 22 34290112 34290143 34327562 34327593 22 34286142 34290143 34327562 272 22 34286715 34286746 34327562 34327593 22 34286715 34290716 34327562 273 16 46394076 46394107 46563367 46563398 16 46394076 46398077 46559397 274 16 46394076 46394107 46645981 46646012 16 46394076 46398077 46642011 275 16 46542432 46542463 46645981 46646012 16 46542432 46546433 46642011 276 7 25985389 25985420 26030197 26030228 7 25981419 25985420 26026227 277 7 25985389 25985420 26109937 26109968 7 25981419 25985420 26105967 278 7 25954012 25954043 25985389 25985420 7 25954012 25958013 25981419 279 16 46563367 46563398 46732957 46732988 16 46559397 46563398 46728987 280 16 46563367 46563398 46724067 46724098 16 46559397 46563398 46724067 281 5 6117034 6117065 6186372 6186403 5 6113064 6117065 6186372 282 4 65366992 65367023 65540791 65540822 4 65366992 65370993 65536821 283 11 25806231 25806262 26002709 26002740 11 25806231 25810232 25998739 284 11 25806231 25806262 26000893 26000924 11 25806231 25810232 26000893 285 7 20278128 20278159 20296076 20296107 7 20274158 20278159 20296076 286 7 20278128 20278159 20380142 20380173 7 20274158 20278159 20376172 287 7 20278128 20278159 20391427 20391458 7 20274158 20278159 20391427 288 7 20278128 20278159 20407650 20407681 7 20274158 20278159 20407650 289 8 3054773 3054804 3172572 3172603 8 3050803 3054804 3168602 290 8 3123415 3123446 3172572 3172603 8 3119445 3123446 3168602 291 1 149873033 149873064 150097137 150097168 1 149873033 149877034 150093167 292 1 149873033 149873064 150110004 150110035 1 149873033 149877034 150106034 293 1 149910043 149910074 150097137 150097168 1 149910043 149914044 150093167 294 1 149910043 149910074 150110004 150110035 1 149910043 149914044 150106034 295 1 149923380 149923411 150110004 150110035 1 149923380 149927381 150106034 296 1 150016977 150017008 150110004 150110035 1 150016977 150020978 150106034 297 1 150032266 150032297 150097137 150097168 1 150032266 150036267 150093167 298 1 150068252 150068283 150110004 150110035 1 150068252 150072253 150106034 299 22 27686269 27686300 27826003 27826034 22 27682299 27686300 27826003 300 20 42100210 42100241 42177997 42178028 20 42096240 42100241 42177997 301 18 67266270 67266301 67320214 67320245 18 67266270 67270271 67316244 302 18 67266270 67266301 67345469 67345500 18 67266270 67270271 67341499 303 18 67266270 67266301 67404406 67404437 18 67266270 67270271 67404406 304 11 20610213 20610244 20630516 20630547 11 20606243 20610244 20626546 305 11 20601546 20601577 20630516 20630547 11 20601546 20605547 20626546 306 11 20630516 20630547 20755854 20755885 11 20626546 20630547 20751884 307 11 29798087 29798118 29826361 29826392 11 29798087 29802088 29822391 308 11 29826361 29826392 29856303 29856334 11 29822391 29826392 29856303 309 25 5777848 5777879 5963748 5963779 25 5777848 5781849 5959778 310 25 5838527 5838558 5963748 5963779 25 5838527 5842528 5959778 311 3 88185502 88185533 88351242 88351273 3 88181532 88185533 88347272 312 11 26381091 26381122 26421158 26421189 11 26381091 26385092 26421158 313 11 26381091 26381122 26552180 26552211 11 26381091 26385092 26552180 314 1 117377450 117377481 117533273 117533304 1 117377450 117381451 117529303 315 1 117501086 117501117 117533273 117533304 1 117501086 117505087 117529303 316 3 40723323 40723354 40842764 40842795 3 40723323 40727324 40838794 317 7 4253429 4253460 4444323 4444354 7 4249459 4253460 4440353 318 27 31943096 31943127 31994751 31994782 27 31943096 31947097 31994751 319 27 31943096 31943127 32006848 32006879 27 31943096 31947097 32006848 320 3 20958830 20958861 21259996 21260027 3 20954860 20958861 21256026

TABLE 33.e6 4 kb Sequence Location N End2 Probe Primer ID-1 257 23192758 PLXDC1_11_23117935_23125158_23188757_23196195_RR OBD RD043.1025 258 103234780 PRKAG2_4_103028895_103043216_103233754_103234780_RF OBD RD043.1029 259 103346193 PRKAG2_4_103028895_103043216_103342192_103345172_RR OBD RD043.1033 260 13854647 PRKCA_11_13786370_13794644_13849517_13854647_RF OBD RD043.1037 261 23695272 PRKCB_13_23475428_23483033_23690253_23695272_RF OBD RD043.1041 262 23695272 PRKCB_13_23532412_23540462_23690253_23695272_RF OBD RD043.1045 263 91981648 RAB33B_2_91817483_91819013_91968018_91981648_FF OBD RD043.1049 264 91972019 RAB33B_2_91817483_91819013_91968018_91981648_RR OBD RD043.1053 265 3072970 RAG2_12_2995445_3004477_3070874_3072970_RF OBD RD043.1057 266 3074875 RAG2_12_2995445_3004477_3070874_3072970_RR OBD RD043.1061 267 3128121 RAG2_12_2995445_3004477_3124836_3128121_RF OBD RD043.1065 268 2779500 RASSF5_5_2727413_2732312_2768970_2779500_FF OBD RD043.1069 269 2865680 RASSF5_5_2727413_2732312_2857276_2865680_FF OBD RD043.1073 270 2779500 RASSF5_5_2752106_2755183_2768970_2779500_FF OBD RD043.1077 271 34331563 RBPJL_22_34286715_34290143_34327562_34334894_FR OBD RD043.1081 272 34331563 RBPJL_22_34286715_34290143_34327562_34334894_RR OBD RD043.1085 273 46563398 SCN10A_16_46394076_46405616_46559136_46563398_RF OBD RD043.1089 274 46646012 SCN10A_16_46394076_46405616_46644599_46646012_RF OBD RD043.1093 275 46646012 SCN10A_16_46542432_46554053_46644599_46646012_RF OBD RD043.1097 276 26030228 SCN2B_7_25981242_25985420_26023779_26030228_FF OBD RD043.1101 277 26109968 SCN2B_7_25981242_25985420_26102356_26109968_FF OBD RD043.1105 278 25985420 SCN4B_7_25954012_25959734_25981242_25985420_RF OBD RD043.1109 279 46732988 SCN5A_16_46559136_46563398_46724067_46732988_FF OBD RD043.1113 280 46728068 SCN5A_16_46559136_46563398_46724067_46732988_FR OBD RD043.1117 281 6190373 SELL_5_6104471_6117065_6186372_6188629_FR OBD RD043.1121 282 65540822 SEPT7_4_65366992_65373527_65534812_65540822_RF OBD RD043.1125 283 26002740 SGCA_11_25806231_25808754_26000893_26002740_RF OBD RD043.1129 284 26004894 SGCA_11_25806231_25808754_26000893_26002740_RR OBD RD043.1133 285 20300077 SIK2_7_20268830_20278159_20296076_20300289_FR OBD RD043.1137 286 20380173 SIK2_7_20268830_20278159_20375473_20380173_FF OBD RD043.1141 287 20395428 SIK2_7_20268830_20278159_20391427_20402715_FR OBD RD043.1145 288 20411651 SIK2_7_20268830_20278159_20407650_20411122_FR OBD RD043.1149 289 3172603 SNAP29_8_3045435_3054804_3164300_3172603_FF OBD RD043.1153 290 3172603 SNAP29_8_3117316_3123446_3164300_3172603_FF OBD RD043.1157 291 150097168 SPRED1_1_149873033_149876737_150087432_150097168_RF OBD RD043.1161 292 150110035 SPRED1_1_149873033_149876737_150099832_150110035_RF OBD RD043.1165 293 150097168 SPRED1_1_149910043_149913663_150087432_150097168_RF OBD RD043.1169 294 150110035 SPRED1_1_149910043_149913663_150099832_150110035_RF OBD RD043.1173 295 150110035 SPRED1_1_149923380_149924915_150099832_150110035_RF OBD RD043.1177 296 150110035 SPRED1_1_150016977_150019540_150099832_150110035_RF OBD RD043.1181 297 150097168 SPRED1_1_150032266_150036031_150087432_150097168_RF OBD RD043.1185 298 150110035 SPRED1_1_150068252_150074099_150099832_150110035_RF OBD RD043.1189 299 27830004 SRC_22_27681702_27686300_27826003_27831147_FR OBD RD043.1193 300 42181998 SRF_20_42097551_42100241_42177997_42186255_FR OBD RD043.1197 301 67320245 STAT1_18_67266270_67281181_67315145_67320245_RF OBD RD043.1201 302 67345500 STAT1_18_67266270_67281181_67340514_67345500_RF OBD RD043.1205 303 67408407 STAT1_18_67266270_67281181_67404406_67407824_RR OBD RD043.1209 304 20630547 STAT3_11_20601546_20610244_20625038_20630547_FF OBD RD043.1213 305 20630547 STAT3_11_20601546_20610244_20625038_20630547_RF OBD RD043.1217 306 20755885 STAT5A_11_20625038_20630547_20748936_20755885_FF OBD RD043.1221 307 29826392 STXBP4_11_29798087_29803880_29820062_29826392_RF OBD RD043.1225 308 29860304 STXBP4_11_29820062_29826392_29856303_29862822_FR OBD RD043.1229 309 5963779 TGFBR1_25_5777848_5781338_5953575_5963779_RF OBD RD043.1233 310 5963779 TGFBR1_25_5838527_5844153_5953575_5963779_RF OBD RD043.1237 311 88351273 TMEM156_3_88174369_88185533_88338789_88351273_FF OBD RD043.1241 312 26425159 TOB1_11_26381091_26387145_26421158_26424834_RR OBD RD043.1245 313 26556181 TOB1_11_26381091_26387145_26552180_26554959_RR OBD RD043.1249 314 117533304 TSPAN3_1_117377450_117387477_117527452_117533304_RF OBD RD043.1253 315 117533304 TSPAN3_1_117501086_117515708_117527452_117533304_RF OBD RD043.1257 316 40842795 TSPAN5_3_40723323_40732311_40838443_40842795_RF OBD RD043.1261 317 4444354 VAV1_7_4248599_4253460_4432636_4444354_FF OBD RD043.1265 318 31998752 VEGFC_27_31943096_31950700_31994751_32003367_RR OBD RD043.1269 319 32010849 VEGFC_27_31943096_31950700_32006848_32015827_RR OBD RD043.1273 320 21260027 ZFHX3_3_20954370_20958861_21248124_21260027_FF OBD RD043.1277

TABLE 33.e7 N Primer Sequence Primer ID-2 Primer Sequence 257 AAGCCACATCCTTCCCACCCAGC OBD RD043.1027 GGAGAGCAAGGTCCTGGGAGTTA 258 GGAAGAGTCCTGACGACATCCTG OBD RD043.1031 GAAGAAATGGTAGTGCCCGCCCC 259 GGGCTGCGGATGCTGTTCCTTGA OBD RD043.1035 GGAAGAGTCCTGACGACATCCTG 260 GTCAACATTTCACTCCGTCGGGC OBD RD043.1039 GGCGAGGCTCTCTCATCTCTCTC 261 CGCCTCAGCGACACAGAGAACAA OBD RD043.1043 CCGTCATAGTTCCCGTCCTGAGG 262 CGCCTCAGCGACACAGAGAACAA OBD RD043.1047 CTGGAGACACGCTGAGGATTGGC 263 AATGCCCTTCCCTAACTCTGAACG OBD RD043.1051 AAACTACAATGAGATAACCACCCT 264 CCAAACTTTTCTGTGGAATACACG OBD RD043.1055 CATAATGAGACTAAATAACTTGTCC 265 CCTGAGCGAGGTCACACTGTTCA OBD RD043.1059 TCCAGAGTGCTTCCTGCCCCAAG 266 TGAGAGCCGCTGGTGTAGATACG OBD RD043.1063 TCCAGAGTGCTTCCTGCCCCAAG 267 GGTGGTGGCTACCCTGAAACTCATTG OBD RD043.1067 TAACAGGTGTGTGTGTAAGAGAGGGA 268 TCCCCTCTCTGGTGCTCCTGACA OBD RD043.1071 ACCCCAGGTTCACGAAAGTCAGG 269 TCCCCTCTCTGGTGCTCCTGACA OBD RD043.1075 AAGGCAGGGAGAGCCAGAGAAGA 270 ACCTTCTGAGCACCTCCCACAGC OBD RD043.1079 GTTTATGTCTTGTTTCTCCTGGACG 271 CTCTGAGTTGCTTACTGCCTCCTGC OBD RD043.1083 CCATTCTGGAAACAATCTGGCAGTA 272 GACAACATACACCTCTCAGACGATGC OBD RD043.1087 CCATTCTGGAAACAATCTGGCAGTA 273 TAGTTTTAGGGCTGGGCACACAGGA OBD RD043.1091 AAAGACAGTAGACACTTCACCAATGA 274 AAGGTGGAGGGTTCAGATGGGCTCAT OBD RD043.1095 AGACTGGCAGGAAATAAACCAAGTTG 275 TCAACAATGCTAAATCACCAAGGG OBD RD043.1099 AGACAGTAGACACTTCACCAATGA 276 TAAGACACAACCCCTGCCACGGG OBD RD043.1103 CCAGGTAACAGGATGGCTCAAGG 277 TAAGACACAACCCCTGCCACGGG OBD RD043.1107 CTCTGTGGTGTCATTGCCCCTTC 278 AGAAGAGTAAGACACAACCCCTGCCA OBD RD043.1111 TGGTCCTGAGACGACTACCTTGAAGT 279 TAGTTTTAGGGCTGGGCACACAGGAG OBD RD043.1115 CTTTAGAGCATACAGTAAGCCAATGG 280 ATGAGAAGGGCAGGACAGGGCTG OBD RD043.1119 CCACCTTTCCGCAGTATCCTCAC 281 GTGATAAGATGGAAGCCAAGACAAAA OBD RD043.1123 GGACGCAGCCATCTTGCCCCGAA 282 TTCCTCTTACCGTCTCTTGCGAT OBD RD043.1127 GTAGAAGTGGGTTTTAGAGAGGGT 283 GCAAGGTTAGTGAGTGGCGAGGT OBD RD043.1131 TGGCTGGACCTGCCTCTCCTTTC 284 TGGCTGGACCTGCCTCTCCTTTC OBD RD043.1135 CAGACCAGCAGCCCTTATGGACA 285 GCAAAATGGGCAGGAAGGACATACAA OBD RD043.1139 GGTTTAGAGGTCCTGATTTGTTCTCC 286 AATGGGCAGGAAGGACATACAAAATA OBD RD043.1143 TGACACTTCTCCCATCAAGAGGG 287 GCAAAATGGGCAGGAAGGACATACAA OBD RD043.1147 CTTGCCCTTGTGGATAGAGAGTAGGC 288 TGGGCAGGAAGGACATACAAAATA OBD RD043.1151 GGGAGATTGGCAACAGATGTAAGC 289 TGTGGAAACAGGAAGGGCACGAC OBD RD043.1155 TCCACCGCATCAGCACCTTCCCA 290 CAGAAGCAACACTTAGGCACCCAG OBD RD043.1159 TCCACCGCATCAGCACCTTCCCA 291 CGCTTTCCTGACCTCCTACCCATCAA OBD RD043.1163 TTTTCATACTTTCCTCTCCTTGCCCC 292 GACAGCCCATAGGTTAGGGACACC OBD RD043.1167 GCTTCCGCCTCCAAATGGCATCT 293 GACAGCCCATAGGTTAGGGACACCAA OBD RD043.1171 TTTTCATACTTTCCTCTCCTTGCCCC 294 CCGCTTTCCTGACCTCCTACCCA OBD RD043.1175 GAGTTCCTTCTTGCTCACGGGTG 295 GACAGCCCATAGGTTAGGGACACC OBD RD043.1179 GAGTTCCTTCTTGCTCACGGGTG 296 GTTAGGGACACCAAATAGTATGCT OBD RD043.1183 TTGAAAGAAATGCCAACAAATGAT 297 GACAGCCCATAGGTTAGGGACACC OBD RD043.1187 GGGCAGAAGTTGAAGCCATCCTG 298 GCTTTCCTGACCTCCTACCCATC OBD RD043.1191 CCCTCTCACATCCCTTGCCCTGT 299 ATCATCCATCCTCACTTGGGCACA OBD RD043.1195 CTTTTGTTAGACAGAAGTTATCAAT 300 TCAAAGCCCAGAATCTCCAGCAT OBD RD043.1199 TACGGGATGAAGTCTGGAGGCAT 301 GCACTAAGAATCAAAGTCGCCTTCCA OBD RD043.1203 CCCAAAAGGCTTCTGACCAACACCTC 302 AAGGCTTCTGACCAACACCTCTGAGA OBD RD043.1207 GAGAATAAATAGGTGATGTGGGAGGC 303 AGGCTGCTGAAGTCCCCGTAGGG OBD RD043.1211 CAAACTCAAGACCTCACATTGTCAGG 304 CCAAGGTGAGTGCCCATCCTCTG OBD RD043.1215 GGTTTGGTGACTTGCTGAAGGGC 305 TACAGTTGGGACCCCTGATTCCG OBD RD043.1219 CCAAGGTGAGTGCCCATCCTCTG 306 CCAAGGTGAGTGCCCATCCTCTG OBD RD043.1223 AGGACCTCAAGGACTTCATCCGC 307 GACTGACCTATGTTGGGAAAAGCAAA OBD RD043.1227 CTAAACAGCATAATACTACTTGCCTC 308 ATGTATGTTTATGTATGACTTCCT OBD RD043.1231 GAATAAAGTAATGTAACAGGAAGA 309 TTTTGCTTGGCTTGCTTCCTTTGGA OBD RD043.1235 ATGTTACTCCGATACTGCTTTCTT 310 GGTTTTCAGCAGATTCTTCCTTGAGG OBD RD043.1239 AGCGGAAGTGCCCCTGCTTTGGTTTA 311 GAACTGCCTACTGCTATGTGAGGATG OBD RD043.1243 GGATGTGTCCAATAACTGGTGGCTGT 312 GGGTGAGGAAGGGACACAGGCAT OBD RD043.1247 GAGAGGGAAGGAGGAAACGAAGC 313 GGGTGAGGAAGGGACACAGGCAT OBD RD043.1251 CTATGTGCTGTGCCAGAGATGGG 314 GAAGTTAGTCCTCACTCTCCTCCC OBD RD043.1255 TCTCCGCCTTGCCAACCCCATCA 315 AAGTTAGTCCTCACTCTCCTCCCA OBD RD043.1259 AAAGTGAGACATTTTAGTGCTCCG 316 CTGCCAATGGAGCAAGAACTTCAAAA OBD RD043.1263 ACAGAACCCGAACAGTCAGACGCTCT 317 GCACCTATTGCCTGTCAAGCCTC OBD RD043.1267 TGGCACCACATCACTCCTGCTGC 318 CGGCTATGTCACTCACTACCTGG OBD RD043.1271 CACTCCACCCTGGCGTGTTTTCC 319 CACCTACGGTCTGATGGTATGTTA OBD RD043.1275 TTTCAGGGCAGAATAAAGATACAT 320 GACACAAATACCAAGGAGAGAAAGGC OBD RD043.1279 CAGAACCTGACTATGTAGGCACGCTG

TABLE 33.e8 N Probe Marker 257 PLXDC1 OBD RD043.1025.1027 258 PRKAG2 OBD RD043.1029.1031 259 PRKAG2 OBD RD043.1033.1035 260 PRKCA OBD RD043.1037.1039 261 PRKCB OBD RD043.1041.1043 262 PRKCB OBD RD043.1045.1047 263 RAB33B OBD RD043.1049.1051 264 RAB33B OBD RD043.1053.1055 265 RAG2 OBD RD043.1057.1059 266 RAG2 OBD RD043.1061.1063 267 RAG2 OBD RD043.1065.1067 268 RASSF5 OBD RD043.1069.1071 269 RASSF5 OBD RD043.1073.1075 270 RASSF5 OBD RD043.1077.1079 271 RBPJL OBD RD043.1081.1083 272 RBPJL OBD RD043.1085.1087 273 SCN10A OBD RD043.1089.1091 274 SCN10A OBD RD043.1093.1095 275 SCN10A OBD RD043.1097.1099 276 SCN2B OBD RD043.1101.1103 277 SCN2B OBD RD043.1105.1107 278 SCN4B OBD RD043.1109.1111 279 SCN5A OBD RD043.1113.1115 280 SCN5A OBD RD043.1117.1119 281 SELL OBD RD043.1121.1123 282 SEPT7 OBD RD043.1125.1127 283 SGCA OBD RD043.1129.1131 284 SGCA OBD RD043.1133.1135 285 SIK2 OBD RD043.1137.1139 286 SIK2 OBD RD043.1141.1143 287 SIK2 OBD RD043.1145.1147 288 SIK2 OBD RD043.1149.1151 289 SNAP29 OBD RD043.1153.1155 290 SNAP29 OBD RD043.1157.1159 291 SPRED1 OBD RD043.1161.1163 292 SPRED1 OBD RD043.1165.1167 293 SPRED1 OBD RD043.1169.1171 294 SPRED1 OBD RD043.1173.1175 295 SPRED1 OBD RD043.1177.1179 296 SPRED1 OBD RD043.1181.1183 297 SPRED1 OBD RD043.1185.1187 298 SPRED1 OBD RD043.1189.1191 299 SRC OBD RD043.1193.1195 300 SRF OBD RD043.1197.1199 301 STAT1 OBD RD043.1201.1203 302 STAT1 OBD RD043.1205.1207 303 STAT1 OBD RD043.1209.1211 304 STAT3 OBD RD043.1213.1215 305 STAT3 OBD RD043.1217.1219 306 STAT5A OBD RD043.1221.1223 307 STXBP4 OBD RD043.1225.1227 308 STXBP4 OBD RD043.1229.1231 309 TGFBR1 OBD RD043.1233.1235 310 TGFBR1 OBD RD043.1237.1239 311 TMEM156 OBD RD043.1241.1243 312 TOB1 OBD RD043.1245.1247 313 TOB1 OBD RD043.1249.1251 314 TSPAN3 OBD RD043.1253.1255 315 TSPAN3 OBD RD043.1257.1259 316 TSPAN5 OBD RD043.1261.1263 317 VAV1 OBD RD043.1265.1267 318 VEGFC OBD RD043.1269.1271 319 VEGFC OBD RD043.1273.1275 320 ZFHX3 OBD RD043.1277.1279

TABLE 34.a Rank N Marker with Dilution Marker Freq Rank Sum Rank Mean Median 1 OBD142_437.439_1.2x OBD142_437.439 1000 198 1.98 2 2 OBD142_025.027_1x OBD142_025.027 1000 1224.5 12.245 8.5 3 OBD142_417.419_1x OBD142_417.419 1000 1369 13.69 13 4 OBD142_517.519_1.2x OBD142_517.519 1000 1251.5 12.515 13 5 OBD142_065.067_1x OBD142_065.067 971 3903 39.03 35.5 6 OBD142_513.515_1.2x OBD142_513.515 971 3903 39.03 35.5 7 OBD142_017.019_1x OBD142_017.019 977 4446 44.46 40 8 OBD142_029.031_1x OBD142_029.031 972 4681.5 46.815 40.5 9 OBD142_069.071_1.2x OBD142_069.071 972 5103.5 51.035 40 10 OBD142_085.087_1.2x OBD142_085.087 972 4667 46.67 41 11 OBD142_093.095_1x OBD142_093.095 1000 3945 39.45 40 12 OBD142_117.119_1.2x OBD142_117.119 1000 4206.5 42.065 38.5 13 OBD142_125.127_1.2x OBD142_125.127 977 4446 44.46 40 14 OBD142_157.159_1.4x OBD142_157.159 1000 3707.5 37.075 38 15 OBD142_233.235_1.4x OBD142_233.235 1000 3707.5 37.075 38 16 OBD142_285.287_1.4x OBD142_285.287 975 4749 47.49 37.75 17 OBD142_325.327_1.4x OBD142_325.327 1000 4206.5 42.065 38.5 18 OBD142_449.451_1x OBD142_449.451 1000 3738 37.38 38.25 19 OBD142_461.463_1.4x OBD142_461.463 972 4667 46.67 41 20 OBD142_469.471_1x OBD142_469.471 975 4749 47.49 37.75 21 OBD142_133.135_1x OBD142_133.135 504 14009 140.09 86.5 22 OBD142_181.183_1.4x OBD142_181.183 504 14009 140.09 86.5 23 OBD142_397.399_1x OBD142_397.399 504 14009 140.09 86.5 24 OBD142_253.255_1.2x OBD142_253.255 867 7643 76.43 109.25 25 OBD142_181.183_1.4x OBD142_181.183 504 14009 140.09 86.5 26 OBD142_037.039_1x OBD142_037.039 779 8626.5 86.265 113 27 OBD142_353.355_1x OBD142_353.355 699 8585.5 85.855 113 28 OBD142_005.007_1x OBD142_005.007 527 12594.5 125.945 76.5 29 OBD142_009.011_1.4x OBD142_009.011 737 9784 97.84 44.5 30 OBD142_025.027_1.2x OBD142_025.027 1000 11604 116.04 42 31 OBD142_029.031_1.4x OBD142_029.031 1000 2760.5 27.605 38 32 OBD142_041.043_1.2x OBD142_041.043 737 9784 97.84 44.5 33 OBD142_045.047_1x OBD142_045.047 525 13251.5 132.515 77.5 34 OBD142_057.059_1.8x OBD142_057.059 715 11959.5 119.595 51.5 35 OBD142_061.063_1.4x OBD142_061.063 814 10698.5 106.985 44.5 36 OBD142_065.067_1.2x OBD142_065.067 1000 859.5 8.595 9.5 37 OBD142_069.071_1.2x OBD142_069.071 967 10625.5 106.255 43 38 OBD142_081.083_1.4x OBD142_081.083 1000 2686 26.86 34 39 OBD142_097.099_1.8x OBD142_097.099 1000 11838 118.38 51.5 40 OBD142_101.103_1x OBD142_101.103 1000 5050 50.5 70 41 OBD142_109.111_1.2x OBD142_109.111 1000 11604 116.04 42 42 OBD142_121.123_1.8x OBD142_121.123 814 10698.5 106.985 44.5 43 OBD142_133.135_1.8x OBD142_133.135 737 9784 97.84 44.5 44 OBD142_137.139_1.2x OBD142_137.139 1000 3052 30.52 39 45 OBD142_141.143_1.4x OBD142_141.143 737 9784 97.84 44.5 46 OBD142_145.147_1.4x OBD142_145.147 523 12431.5 124.315 81.5 47 OBD142_153.155_1.4x OBD142_153.155 1000 914 9.14 10 48 OBD142_157.159_1.4x OBD142_157.159 514 13293.5 132.935 83.5 49 OBD142_165.167_1x OBD142_165.167 1000 4818.5 48.185 69.5 50 OBD142_185.187_1.4x OBD142_185.187 1000 3161 31.61 39 51 OBD142_189.191_1x OBD142_189.191 1000 2760.5 27.605 38 52 OBD142_197.199_1.4x OBD142_197.199 1000 2795 27.95 38 53 OBD142_201.203_1.4x OBD142_201.203 1000 2903.5 29.035 38.5 54 OBD142_213.215_1.4x OBD142_213.215 151 19515.5 195.155 212 55 OBD142_233.235_1.2x OBD142_233.235 505 12737 127.37 81.5 56 OBD142_241.243_1x OBD142_241.243 1000 2820.5 28.205 38 57 OBD142_253.255_1.2x OBD142_253.255 1000 5334.5 53.345 70 58 OBD142_257.259_1.2x OBD142_257.259 1000 11995.5 119.955 51.5 59 OBD142_261.263_1x OBD142_261.263 1000 5144 51.44 69.5 60 OBD142_265.267_1.4x OBD142_265.267 967 9975.5 99.755 41.5 61 OBD142_273.275_1.4x OBD142_273.275 962 12527 125.27 51.5 62 OBD142_277.279_1.2x OBD142_277.279 1000 3060 30.6 38.5 63 OBD142_297.299_1.2x OBD142_297.299 1000 847.5 8.475 9.5 64 OBD142_309.311_1.4x OBD142_309.311 806 9550 95.5 42 65 OBD142_313.315_1x OBD142_313.315 1000 2760.5 27.605 38 66 OBD142_321.323_1.2x OBD142_321.323 1000 11995.5 119.955 51.5 67 OBD142_325.327_1.2x OBD142_325.327 1000 4958.5 49.585 69.5 68 OBD142_329.331_1.4x OBD142_329.331 1000 2795 27.95 38 69 OBD142_337.339_1x OBD142_337.339 817 10759.5 107.595 43 70 OBD142_357.359_1.4x OBD142_357.359 962 12527 125.27 51.5 71 OBD142_361.363_1.2x OBD142_361.363 932 11406.5 114.065 43 72 OBD142_373.375_1x OBD142_373.375 1000 2903.5 29.035 38.5 73 OBD142_393.395_1.2x OBD142_393.395 1000 921.5 9.215 10.5 74 OBD142_401.403_1x OBD142_401.403 1000 2820.5 28.205 38 75 OBD142_405.407_1x OBD142_405.407 537 11739.5 117.395 73.5 76 OBD142_413.415_1.2x OBD142_413.415 638 10473 104.73 45.5 77 OBD142_433.435_1x OBD142_433.435 1000 2969.5 29.695 39 78 OBD142_437.439_1x OBD142_437.439 1000 5144 51.44 69.5 79 OBD142_445.447_1.2x OBD142_445.447 752 10351.5 103.515 45 80 OBD142_457.459_1x OBD142_457.459 1000 3016 30.16 38.5 81 OBD142_469.471_1.2x OBD142_469.471 1000 2829 28.29 38.5 82 OBD142_477.479_1.2x OBD142_477.479 752 10351.5 103.515 45 83 OBD142_489.491_1x OBD142_489.491 937 9975.5 99.755 41.5 84 OBD142_501.503_1x OBD142_501.503 537 11739.5 117.395 73.5 85 OBD142_509.511_1.8x OBD142_509.511 970 11725.5 117.255 43.25 86 OBD142_517.519_1x OBD142_517.519 1000 914 9.14 10

TABLE 34.b N Mean p value Median p value Classification 1 0.01576 0.01562 Present in Strength Training 2 0.08678 0.09375 Present in Strength Training 3 0.09328 0.125 Present in Strength Training 4 0.09312 0.125 Present in Strength Training 5 0.20758 0.13696 Present in Strength Training 6 0.20758 0.13696 Present in Strength Training 7 0.23382 0.28125 Present in Strength Training 8 0.23992 0.28125 Present in Strength Training 9 0.26566 0.28125 Present in Strength Training 10 0.24252 0.28125 Present in Strength Training 11 0.22246 0.28125 Present in Strength Training 12 0.23621 0.28125 Present in Strength Training 13 0.23382 0.28125 Present in Strength Training 14 0.22324 0.28125 Present in Strength Training 15 0.22324 0.28125 Present in Strength Training 16 0.24953 0.28125 Present in Strength Training 17 0.23621 0.28125 Present in Strength Training 18 0.21652 0.28125 Present in Strength Training 19 0.24252 0.28125 Present in Strength Training 20 0.24953 0.28125 Present in Strength Training 21 0.60112 0.34375 Present in Strength Training 22 0.60112 0.34375 Present in Strength Training 23 0.60112 0.34375 Present in Strength Training 24 0.62216 0.34375 Present in Strength Training 25 0.60112 0.34375 Present in Strength Training 26 0.35984 0.45312 Present in Strength Training 27 0.35078 0.45312 Present in Strength Training 28 0.57 0.28906 Present in Endurance Training 29 0.4475 0.1875 Present in Endurance Training 30 0.53687 0.1875 Present in Endurance Training 31 0.13594 0.1875 Present in Endurance Training 32 0.4475 0.1875 Present in Endurance Training 33 0.60297 0.28906 Present in Endurance Training 34 0.55312 0.1875 Present in Endurance Training 35 0.49625 0.1875 Present in Endurance Training 36 0.05469 0.07031 Present in Endurance Training 37 0.48812 0.1875 Present in Endurance Training 38 0.13008 0.1875 Present in Endurance Training 39 0.545 0.1875 Present in Endurance Training 40 0.21125 0.28906 Present in Endurance Training 41 0.53687 0.1875 Present in Endurance Training 42 0.49625 0.1875 Present in Endurance Training 43 0.4475 0.1875 Present in Endurance Training 44 0.14414 0.1875 Present in Endurance Training 45 0.4475 0.1875 Present in Endurance Training 46 0.56711 0.28906 Present in Endurance Training 47 0.05781 0.07031 Present in Endurance Training 48 0.6025 0.28906 Present in Endurance Training 49 0.20031 0.28906 Present in Endurance Training 50 0.15117 0.1875 Present in Endurance Training 51 0.13594 0.1875 Present in Endurance Training 52 0.13711 0.1875 Present in Endurance Training 53 0.1418 0.1875 Present in Endurance Training 54 0.90047 1 Present in Endurance Training 55 0.57758 0.28906 Present in Endurance Training 56 0.13828 0.1875 Present in Endurance Training 57 0.22125 0.28906 Present in Endurance Training 58 0.55312 0.1875 Present in Endurance Training 59 0.21031 0.28906 Present in Endurance Training 60 0.46375 0.1875 Present in Endurance Training 61 0.58562 0.1875 Present in Endurance Training 62 0.14766 0.1875 Present in Endurance Training 63 0.05531 0.07031 Present in Endurance Training 64 0.43937 0.1875 Present in Endurance Training 65 0.13594 0.1875 Present in Endurance Training 66 0.55312 0.1875 Present in Endurance Training 67 0.20344 0.28906 Present in Endurance Training 68 0.13711 0.1875 Present in Endurance Training 69 0.49625 0.1875 Present in Endurance Training 70 0.58562 0.1875 Present in Endurance Training 71 0.52875 0.1875 Present in Endurance Training 72 0.1418 0.1875 Present in Endurance Training 73 0.05781 0.07031 Present in Endurance Training 74 0.13828 0.1875 Present in Endurance Training 75 0.5257 0.28906 Present in Endurance Training 76 0.48812 0.1875 Present in Endurance Training 77 0.14297 0.1875 Present in Endurance Training 78 0.21031 0.28906 Present in Endurance Training 79 0.48 0.1875 Present in Endurance Training 80 0.14414 0.1875 Present in Endurance Training 81 0.13594 0.1875 Present in Endurance Training 82 0.48 0.1875 Present in Endurance Training 83 0.46375 0.1875 Present in Endurance Training 84 0.5257 0.28906 Present in Endurance Training 85 0.545 0.1875 Present in Endurance Training 86 0.05781 0.07031 Present in Endurance Training

TABLE 35 N Equine Marker Exact_Boschloo_p.value 1 OBD154_001/OBD154_003_1:2x 0.597203758 2 OBD154_009/OBD154_011_1:2x 0.180069259 3 OBD154_013/OBD154_015_1x 0.050106528 4 OBD154_033/OBD154_035_1:4x 0.283703806 5 OBD154_037/OBD154_039_1:8x 0.523402567 6 OBD154_041/OBD154_043_1x 0.64299739 7 OBD154_045/OBD154_047_1x 0.180069259 8 OBD154_049/OBD154_051_1:4x 0.11992508 9 OBD154_053/OBD154_055_1:2x 0.597203758 10 OBD154_057/OBD154_059_1:2x 0.663949317 11 OBD154_061/OBD154_063_1x 0.663949317 12 OBD154_069/OBD154_071_1x 0.23718116 13 OBD154_073/OBD154_075_1x 0.125083174 14 OBD154_077/OBD154_079_1x 0.422463565 15 OBD154_085/OBD154_087_1:2x 0.038860637 16 OBD154_093/OBD154_095_1:2x 0.075142123 17 OBD154_097/OBD154_099_1x 0.523402567 18 OBD154_105/OBD154_107_1:2x 0.210490032 19 OBD154_109/OBD154_111_1:2x 0.387940572 20 OBD154_113/OBD154_115_1:4x 0.523402567 21 OBD154_117/OBD154_119_1x 0.659282164 22 OBD154_121/OBD154_123_1x 0.659282164 23 OBD154_125/OBD154_127_1:2x 0.006313179 24 OBD154_133/OBD154_135_1:2x 0.32961205 25 OBD154_137/OBD154_139_1x 0.663949317 26 OBD154_141/OBD154_143_1x 0.180069259 27 OBD154_149/OBD154_151_1:2x 0.678620772 28 OBD154_153/OBD154_155_1:8x 0.523402567 29 OBD154_157/OBD154_159_1:2x 0.038860637 30 OBD154_161/OBD154_163_1:2x 0.422463565 31 OBD154_165/OBD154_167_1x 0.180069259 32 OBD154_169/OBD154_171_1:4x 0.283703806 33 OBD154_177/OBD154_179_1x 0.23718116 34 OBD154_185/OBD154_187_1x 0.64299739 35 OBD154_201/OBD154_203_1x 0.11992508 36 OBD154_205/OBD154_207_1:2x 0.125083174 37 OBD154_209/OBD154_211_1:2x 0.253032887 38 OBD154_213/OBD154_215_1:2x 0.180069259 39 OBD154_217/OBD154_219_1x 0.387940572 40 OBD154_229/OBD154_231_1x 0.054191604 41 OBD154_237/OBD154_239_1x 0.23718116 42 OBD154_245/OBD154_247_1x 0.050106528

TABLE 36 Top Human Markers (from I to IIIB) Odds N Marker for Human Training Ratio Combined Cardio Strength 1 OBD142_029.031_1x Any 7.2 0.01668097 0.066688 0.01613009 2 OBD142_061.063_1.8x Any 8.2 0.01851064 0.11741215 0.10680154 3 OBD142_069.071_1.2x Any 8 0.00255609 0.066688 0.05766889 4 OBD142_089.091_1x Any 2.9 0.12375267 0.40122897 0.18059725 5 OBD142_137.139_1.2x Any 8 0.06270144 0.11741215 0.18262433 6 OBD142_081.083_1.4x Endurance 6 0.13923948 0.070484 0.7999889 7 OBD142_189.191_1x Endurance 4.5 0.11969458 0.11741215 0.84528948 8 OBD142_213.215_1.4x Endurance 2.25 1 0.69409048 0.13523206 9 OBD142_017.019_1.2x Strength 4 0.72495046 0.54542431 0.28124028 10 OBD142_037.039_1x Strength 12 0.15251771 1 0.02525659 11 OBD142_065.067_1x Strength 5 0.13191103 0.54542431 0.05766889 12 OBD142_133.135_1x Strength 4 0.46156086 1 0.01613009 13 OBD142_253.255_1.2x Strength 12 0.44960749 0.61010368 0.02421162 14 OBD142_353.355_1x Strength 9 0.11969458 1 0.01615402 15 OBD142_477.479_1x Strength 9 0.42751765 1 0.02525659 16 OBD142_181.183_1.4x Strength 2 0.75595814 0.74070856 0.17780781 17 OBD142_397.399_1x Strength 2 0.15163712 0.66842823 0.09667637 Table 37 is shown below. Some parts of the table have been left out which relate to information shown in other tables.

TABLE 37.A1 Loop probe GeneLocus detected 1 ACACB_12_109146008_109150083_109185066_109187324_RR ACACB E_Trn 2 ACBD6_1_180269638_180272765_180371571_180375410_RR ACBD6 E_Trn 3 ACBD6_1_180337907_180340909_180371571_180375410_FR ACBD6 E_Trn 4 ADRB3_8_37962724_37965269_37984580_37986052_FF ADRB3 Str_Trn 5 ADRB3_8_37962724_37965269_37996522_37999233_FR ADRB3 Str_Trn 6 ALDH1A2_15_58053198_58062371_58157807_58162832_RR ALDH1A2 Str_Trn 7 ALDH1A2_15_58053198_58062371_58229591_58234474_RF ALDH1A2 E_Trn 8 ANO2_12_5767708_5775129_5922387_5930466_RR ANO2 Str_Trn 9 ANO2_12_5872622_5877860_5922387_5930466_RR ANO2 Str_Trn 10 B3GAT1_11_134376219_134382136_134419343_134423366_FF B3GAT1 Str_Trn 11 B3GAT2_6_70837358_70839856_70855194_70857991_FR B3GAT2 E_Trn 12 B3GAT2_6_70837358_70839856_70933019_70941366_FF B3GAT2 Str_Ctrl 13 BMP7_20_57274840_57277666_57290751_57294583_RF BMP7 E_Ctrl 14 C1GALT1_7_7113076_7114831_7258228_7260668_FF C1GALT1 E_Trn 15 CALCR_7_93553156_93563952_93593898_93597071_RF CALCR E_Ctrl 16 CARD11_7_2966372_2970772_3066095_3073017_RR CARD11 E_Trn 17 CASP9_1_15526774_15533191_15569002_15572579_FR CASP9 E_Trn 18 CBL_11_119249760_119252653_119294588_119299643_RF CBL E_Trn 19 CD36_7_80539507_80544315_80603212_80611693_FR CD36 E_Ctrl 20 CD36_7_80539507_80544315_80679651_80687690_FR CD36 Str_Ctrl 21 COL13A1_10_69769669_69775141_69840301_69843474_RF COL13A1 E_Trn 22 COL25A1_4_109024771_109031337_109090838_109104305_RR COL25A1 E_Ctrl 23 COL25A1_4_109090838_109104305_109307411_109309712_RF COL25A1 E_Ctrl 24 COL4A2_13_110272408_110277108_110487749_110493325_FR COL4A2 E_Trn 25 COL5A1_9_134738485_134741113_134811418_134816113_RR COL5A1 Str_Trn 26 CYGB_17_76511049_76513649_76555120_76557454_RF CYGB Str_Trn 27 CYGB_17_76533052_76534398_76555120_76557454_RF CYGB Str_Trn 28 CYGB_17_76555120_76557454_76593886_76595265_FF CYGB Str_Trn 29 CYGB_17_76555120_76557454_76593886_76595265_FR CYGB Str_Trn

TABLE 37.B1 30 DGKH_13_42011104_42015078_42235825_42240914_RR DGKH E_Trn 31 DIAPH3_13_59818047_59823591_59854837_59860534_RR DIAPH3 E_Ctrl 32 DKK3_11_11956071_11968035_11984245_11993733_FR DKK3 Str_Trn 33 DKK3_11_11956071_11968035_12010923_12019458_FF DKK3 Str_Trn 34 DKK3_11_11956071_11968035_12010923_12019458_FR DKK3 Str_Trn 35 DKK3_11_11956071_11968035_12048403_12051930_FR DKK3 Str_Trn 36 DLK1_14_100687837_100692867_100749541_100751577_RF DLK1 Str_Trn 37 DOK5_20_54466479_54470848_54572383_54577350_RF DOK5 Str_Ctrl 38 EGR3_8_22681793_22682820_22737091_22739184_FF EGR3 E_Trn 39 EHD1_11_64868178_64874017_64914431_64916090_RF EHD1 E_Trn 40 EMCN_4_100525710_100532027_100732651_100738720_RR EMCN Str_Ctrl 41 ETS1_11_128476761_128480323_128561632_128566579_RR ETS1 E_Trn 42 EYA1_8_71216399_71218728_71261816_71267769_RR EYA1 Str_Trn 43 FBLN2_3_13512352_13515076_13582406_13590343_RF FBLN2 E_Trn 44 FBXO32_8_123526212_123527874_123555254_123559065_FR FBXO32 E_Trn 45 FOXO1_13_40524349_40526124_40688580_40690771_RR FOXO1 Str_Ctrl 46 FOXO3_6_108603215_108604436_108629992_108635481_FR FOXO3 E_Trn_(—) 47 FTO_16_53844989_53854574_54045378_54052319_RF FTO E_Trn 48 GPC5_13_91724432_91728749_91910388_91925040_FR GPC5 E_Trn 49 GPC5_13_91794062_91815301_91953115_91957441_RR GPC5 E_Trn 50 GPC6_13_94054831_94060621_94121445_94133208_RF GPC6 Str_Ctrl 51 GPC6_13_94121445_94133208_94296633_94304225_FF GPC6 Str_Ctrl 52 GRB10_7_50706363_50709345_50775503_50780905_RF GRB10 E_Trn 53 GSN_9_121177548_121180410_121268506_121274144_FR GSN E_Trn 54 GSN_9_121182946_121189020_121239116_121243347_FF GSN Str_Ctrl 55 GSN_9_121227501_121232628_121268506_121274144_FR GSN E_Trn 56 GSN_9_121239116_121243347_121268506_121274144_FR GSN E_Trn 57 GSN_9_121253564_121256485_121268506_121274144_RR GSN Str_Trn 58 HDAC9_7_18055950_18064786_18135886_18142010_RF HDAC9 E_Ctrl 59 HOXC6_12_53956382_53960014_53992251_53994278_FF HOXC6 Str_Trn

TABLE 37.C1 60 IGF1R_15_98659065_98662585_98893484_98899517_FR IGF1R E_Trn 61 IL1RAP_3_190465562_190469171_190489665_190498302_RF IL1RAP E_Trn 62 IL1RAP_3_190489665_190498302_190560851_190563356_FR IL1RAP E_Ctrl 63 KDM1A_1_23064655_23070269_23096951_23098159_FR KDM1A Str_Ctrl 64 LAMA2_6_128920996_128927003_129105731_129113311_FF LAMA2 E_Trn 65 LAMA2_6_129342029_129351351_129383008_129389769_FR LAMA2 E_Trn 66 LCK_1_32214585_32217213_32237144_32241139_RF LCK E_Ctrl 67 LDB2_4_16489298_16494220_16535160_16542582_RR LDB2 E_Ctrl 68 LMO4_1_87315524_87318670_87343110_87349940_FF LMO4 E_Trn 69 LMO4_1_87315524_87318670_87355277_87360229_FR LMO4 Str_Trn 70 MAPK10_4_86572598_86581486_86617317_86621940_FF MAPK10 E_Trn_(—) 71 MBNL1_3_152229500_152234786_152252961_152257281_FR MBNL1 E_Trn 72 MBNL1_3_152229500_152234786_152281057_152285843_FR MBNL1 Str_Trn 73 MYBPC1_12_101527342_101530065_101646571_101655128_RF MYBPC1 Str_Ctrl 74 MYH1_17_10491098_10496051_10520297_10523271_RR MYH1 Str_Trn 75 MYH1_17_10523271_10524567_10560779_10565755_FF MYH1 E_Ctrl 76 MYO18B_22_26004818_26009467_26030914_26037279_FF MYO18B E_Trn 77 NCAM1_11_113019160_113028536_113163748_113168132_FR NCAM1 E_Trn 78 NECTIN2_19_44815042_44816736_44827160_44828776_RR NECTIN2 E_Ctrl 79 NFKB1_4_102504137_102509238_102557818_102560252_FF NFKB1 Str_Ctrl 80 NFKB1_4_102557818_102560252_102627099_102634363_FR NFKB1 E_Trn 81 NFKB1_4_102599188_102601960_102627099_102634363_FR NFKB1 E_Trn 82 NR4A1_12_51995149_51997631_52041793_52046779_RR NR4A1 Str_Trn 83 NRXN1_2_50580957_50583587_50867546_50884047_RF NRXN1 E_Ctrl 84 NTRK2_9_84804816_84814325_84917519_84924935_FR NTRK2 E_Ctrl 85 NTRK2_9_84804816_84814325_84934592_84942655_RF NTRK2 E_Ctrl 86 PAG1_8_81007411_81018107_81069439_81070856_FR PAG1 E_Trn 87 PAG1_8_81007411_81018107_81126745_81129448_FR PAG1 E_Trn 88 PCK1_20_57527297_57530814_57551578_57557205_RR PCK1 E_Trn 89 PCK1_20_57527297_57530814_57570220_57572870_RR PCK1 E_Trn

TABLE 37.E1 90 PCK1_20_57527297_57530814_57579772_57583521_RR PCK1 E_Trn 91 PCK1_20_57527297_57530814_57583521_57585923_RR PCK1 Str_Trn 92 PDK3_X_24441637_24447950_24480152_24481252_FR PDK3 E_Trn 93 PDK3_X_24441637_24447950_24490440_24491541_FR PDK3 E_Trn 94 PHTF2_7_77800747_77805972_77956111_77960107_RR PHTF2 E_Trn 95 PHTF2_7_77846910_77851576_77956111_77960107_RR PHTF2 Str_Ctrl 96 PIK3C3_18_42033052_42039159_42070009_42072187_RF PIK3C3 Str_Ctrl 97 PIK3C3_18_42070009_42072187_42088671_42094691_FF PIK3C3 E_Ctrl 98 PIK3R1_5_68187850_68194388_68237549_68241297_FF PIK3R1 E_Trn 99 PIK3R1_5_68203536_68213336_68237549_68241297_FR PIK3R1 E_Trn 100 PLCXD2_3_111719030_111722119_111809065_111815838_RR PLCXD2 E_Ctrl 101 PPARGC1A_4_23871872_23880181_23925180_23932379_FF PPARGC1A E_Ctrl 102 PPP3CA_4_101055418_101067369_101247819_101259416_RR PPP3CA E_Trn 103 PRDX6_1_173434669_173438537_173475099_173476805_FR PRDX6 E_Trn 104 PRDX6_1_173434669_173438537_173477717_173485417_FR PRDX6 E_Trn 105 PRDX6_1_173450908_173452763_173477717_173485417_FR PRDX6 Str_Trn 106 PRKCCL10_6432893_6439235_6488207_6489596_FF PRKCQ E_Trn 107 PTPRC_1_198595771_198598296_198659753_198666156_RF PTPRC E_Ctrl 108 PTPRC_1_198631562_198634915_198659753_198666156_RF PTPRC E_Ctrl 109 PTPRC_1_198659753_198666156_198697386_198704777_FR PTPRC E_Ctrl 110 PTPRC_1_198659753_198666156_198704777_198709653_FR PTPRC E_Ctrl 111 PTPRC_1_198659753_198666156_198721093_198724578_FF PTPRC E_Ctrl 112 PTPRC_1_198659753_198666156_198768850_198775826_FF PTPRC E_Ctrl 113 PYGM_11_64747174_64749438_64762879_64765587_RF PYGM E_Trn 114 RGS6_14_72139099_72144564_72213251_72222544_FR RGS6 Str_Ctrl 115 RORA_15_60902137_60909221_61019417_61030714_RR RORA E_Trn 116 RUNX3_1_24920810_24923822_24973522_24976037_RF RUNX3 Str_Ctrl 117 RYR1_19_38410632_38413089_38495982_38499305_RR RYR1 Str_Ctrl 118 SGCZ_8_14631157_14642508_14656955_14664444_RF SGCZ E_Trn 119 SLC35B1_17_49700402_49702340_49724264_49725934_RR SLC35B1 Str_Trn 120 SLC35D1_1_66998822_67004850_67070417_67074223_FR SLC35D1 E_Ctrl 121 SMAD7_18_48917335_48920290_48969505_48974578_RF SMAD7 Str_Ctrl 122 STIM1_11_4071215_4074242_4084365_4091420_FR STIM1 E_Trn 123 STK39_2_167959346_167965882_168109573_168114525_FF STK39 E_Trn 124 STK39_2_168057412_168062336_168109573_168114525_FF STK39 E_Trn 125 STXBP4_17_55035186_55042800_55142272_55149288_FR STXBP4 E_Trn 126 SULF2_20_47663998_47665865_47797013_47801718_FR SULF2 Str_Trn 127 SYK_9_90789107_90793598_90876350_90879196_RF SYK E_Trn 128 SYK_9_90816328_90822228_90832284_90836084_RR SYK E_Ctrl 129 SYK_9_90816328_90822228_90836573_90843345_FR SYK E_Trn 130 SYK_9_90816328_90822228_90836573_90843345_RR SYK E_Ctrl 131 SYK_9_90816328_90822228_90872966_90875740_RR SYK E_Ctrl 132 TBX21_17_47685438_47687129_47704291_47707744_FR TBX21 Str_Trn 133 TGFB2_1_218317687_218325587_218386401_218389011_FR TGFB2 E_Trn 134 TGFBR2_3_30563062_30565548_30608158_30611268_FF TGFBR2 E_Trn 135 TGFBR2_3_30566144_30567439_30633318_30636860_RR TGFBR2 Str_Ctrl 136 TGFBR2_3_30566144_30567439_30694718_30698514_RR TGFBR2 Str_Ctrl 137 TGFBR2_3_30641481_30645057_30688470_30694718_FF TGFBR2 E_Trn 138 THADA_2_43260154_43263093_43324949_43335508_FF THADA Str_Trn 139 THADA_2_43260154_43263093_43415062_43421910_FF THADA Str_Trn 140 THNSL2_2_88139809_88146295_88161717_88164554_FF THNSL2 E_Ctrl 141 THNSL2_2_88139809_88146295_88161717_88164554_FR THNSL2 E_Ctrl 142 TLR2_4_153659613_153661830_153693586_153700349_RF TLR2 Str_Ctrl 143 TNFRSF25_1_6481328_6484248_6494588_6498048_FR TNFRSF25 Str_Trn 144 TTN_2_178554164_178555670_178788193_178796485_FR TTN E_Ctrl 145 UACA_15_70715123_70719636_70780754_70784668_RF UACA E_Trn 146 WASL_7_123664155_123666896_123763390_123768284_RF WASL E_Trn 147 ZEB1_10_31273317_31275631_31437913_31439545_RF ZEB1 E_Ctrl 148 ZEB1_10_31273317_31275631_31507470_31524442_FF ZEB1 E_Ctrl 149 ZEB1_10_31437913_31439545_31458964_31462037_FR ZEB1 E_Ctrl 150 ZEB1_10_31437913_31439545_31463562_31470397_FR ZEB1 E_Ctrl 151 ZFHX3_16_73147488_73153243_73182254_73184585_FF ZFHX3 Str_Trn 152 ADRB3_8_37962724_37965269_37987735_37989039_FR ADRB3 Str_Trn 153 ADRB3_8_37962724_37965269_38014799_38016599_FR ADRB3 Str_Trn 154 AGT_1_230717799_230719628_230752057_230757333_RF AGT Str_Trn 155 AGT_1_230724515_230729957_230752057_230757333_RF AGT Str_Trn 156 BMPR1B_4_94967703_94973952_95026184_95035151_FR BMPR1B Str_Trn 157 HTR2A_13_46860092_46866824_46904346_46907815_RF HTR2A Str_Trn 158 PPARA_22_46101029_46102611_46241078_46244347_FR PPARA E_Trn 159 SOS1_2_38982199_38993639_39061418_39066028_FF SOS1 Str_Trn 160 SVEP1_9_110493529_110499578_110527410_110532406_FR SVEP1 Str_Trn 161 UBE3A_15_25355032_25368345_25399797_25404434_FF UBE3A Str_Trn 162 UBE3A_15_25355032_25368345_25457129_25464700_FR UBE3A Str_Trn 163 ACBD6_1_180431719_180434683_180541491_180549122_RR ACBD6 E_Trn 164 BMPR1B_4_94821712_94826817_94866803_94871889_FF BMPR1B Str_Trn 165 HADHA_2_26188355_26191067_26247231_26249308_FR HADHA Str_Trn 166 HADHA_2_26188355_26191067_26280650_26284864_FF HADHA Str_Trn 167 MTFR1_8_65658401_65661888_65780891_65782535_RF MTFR1 E_Trn 168 MYBPC1_12_101567479_101571538_101655128_101656342_RF MYBPC1 Str_Trn 169 MYH1_17_10502067_10505465_10533547_10534931_RF MYH1 Str_Trn 170 MYL1_2_210288997_210291732_210359762_210362293_FF MYL1 E_Trn 171 MYOD1_11_17685862_17689487_17729653_17733608_FR MYOD1 E_Trn 172 NECTIN3_3_111028574_111034204_111209684_111210764_FR NECTIN3 Str_Trn 173 PON1_7_95303795_95305644_95332254_95337348_RF PON1 Str_Trn 174 ACACB_12_109146008_109150083_109236052_109237242_RR ACACB E_Ctrl 175 ACACB_12_109236052_109237242_109268078_109273323_RR ACACB E_Ctrl 176 COL1A2_7_94359704_94366215_94394399_94397338_RF COL1A2 E_Ctrl 177 COX6A1_12_120397017_120399520_120449180_120450939_RF COX6A1 E_Ctrl 178 GGPS1_1_235284158_235288561_235306299_235310474_FR GGPS1 E_Ctrl 179 GSN_9_121182946_121189020_121323589_121328431_FF GSN Str_Trn_(—)

TABLE 37.F2 180 HTR2A_13_46847106_46857832_46938758_46942222_RF HTR2A E_Ctrl 181 HTR2A_13_46877712_46880636_46938758_46942222_FF HTR2A E_Ctrl 182 IGF1R_15_98652565_98657862_98731539_98737034_RF IGF1R Str_Trn 183 MUSK_9_110648469_110652659_110747866_110751903_FR MUSK Str_Trn_(—) 184 MYOT_5_137829466_137834410_137882068_137884626_RR MYOT E_Ctrl 185 PPARA_22_46128634_46134707_46231440_46235124_FR PPARA Str_Trn 186 PPP1R9A_7_94903925_94908776_94951930_94967018_RF PPP1R9A E_Ctrl 187 PPP1R9A_7_94951930_94967018_95061734_95065150_FR PPP1R9A E_Ctrl 188 PPP1R9A_7_94951930_94967018_95258927_95267729_FF PPP1R9A E_Ctrl 189 RB1_13_48378062_48381344_48486008_48495146_FF RB1 E_Ctrl 190 SLC25A13_7_96209525_96214524_96295606_96302029_FF SLC25A13 E_Ctrl 191 ACE2_X_15558483_15561359_15624288_15632375_RR ACE2 E_Ctrl 192 DNAH5_5_13907228_13913186_13947622_13950495_FR DNAH5 E_Ctrl 193 EMCN_4_100636305_100649860_100744427_100745788_RR EMCN E_Ctrl 194 ITGAV_2_186622411_186639782_186682119_186696186_RR ITGAV E_Ctrl 195 MSTN_2_190044593_190053476_190068550_190073029_FR MSTN E_Ctrl 196 PLCXD2_3_111633890_111638317_111672672_111677327_FR PLCXD2 E_Ctrl 197 SGCZ_8_14631157_14642508_14778176_14785491_FF SGCZ E_Ctrl 198 SLC25A13_7_96178122_96182739_96295606_96302029_RF SLC25A13 E_Ctrl 199 SOCS7_17_38347510_38348776_38360864_38363420_FR SOCS7 E_Ctrl 200 SRI_7_88199682_88203042_88229166_88237101_RF SRI E_Ctrl 201 STXBP4_17_55035186_55042800_55117598_55123347_RR STXBP4 E_Ctrl 202 SVEP1_9_110397951_110405969_110503630_110509758_FF SVEP1 E_Ctrl Table 38 is below. Some parts of the table have been left out which relates to information in other tables.

TABLE 38.a Loop Probe GeneLocus Detected 1 C1GALT1_7_7113076_7114831_7258228_7260668_FF C1GALT1 E_Trn 2 DKK3_11_11956071_11968035_11984245_11993733_FR DKK3 Str_Trn 3 FBXO32_8_123526212_123527874_123555254_123559065_FR FBXO32 E_Trn 4 GPC6_13_94054831_94060621_94121445_94133208_RF GPC6 Str_Ctrl 5 GSN_9_121177548_121180410_121268506_121274144_FR GSN E_Trn 6 LMO4_1_87315524_87318670_87343110_87349940_FF LMO4 E_Trn 7 MAPK10_4_86572598_86581486_86617317_86621940_FF MAPK10 E_Trn 8 MBNL1_3_152229500_152234786_152281057_152285843_FR MBNL1 Str_Trn 9 PCK1_20_57527297_57530814_57579772_57583521_RR PCK1 E_Trn 10 PIK3C3_18_42070009_42072187_42088671_42094691_FF PIK3C3 E_Ctrl 11 PTPRC_1_198595771_198598296_198659753_198666156_RF PTPRC E_Ctrl 12 RGS6_14_72139099_72144564_72213251_72222544_FR RGS6 Str_Ctrl 13 RUNX3_1_24920810_24923822_24973522_24976037_RF RUNX3 Str_Ctrl 14 ZFHX3_16_73147488_73153243_73182254_73184585_FF ZFHX3 Str_Trn 15 MYOT_5_137829466_137834410_137882068_137884626_RR MYOT Str_Ctrl 16 AGT_1_230724515_230729957_230752057_230757333_RF AGT Str_Trn 17 MYL1_2_210288997_210291732_210359762_210362293_FF MYL1 E_Trn 18 SRI_7_88199682_88203042_88229166_88237101_RF SRI E_Ctrl

TABLE 38.g Inner_primers Probe PCR-Primer1_ID 1 C1GALT1_7_7113076_7114831_7258228_7260668_FF OBD142_025 2 DKK3_11_11956071_11968035_11984245_11993733_FR OBD142_061 3 FBXO32_8_123526212_123527874_123555254_123559065_FR OBD142_089 4 GPC6_13_94054831_94060621_94121445_94133208_RF OBD142_109 5 GSN_9_121177548_121180410_121268506_121274144_FR OBD142_117 6 LMO4_1_87315524_87318670_87343110_87349940_FF OBD142_145 7 MAPK10_4_86572598_86581486_86617317_86621940_FF OBD142_153 8 MBNL1_3_152229500_152234786_152281057_152285843_FR OBD142_157 9 PCK1_20_57527297_57530814_57579772_57583521_RR OBD142_189 10 PIK3C3_18_42070009_42072187_42088671_42094691_FF OBD142_213 11 PTPRC_1_198595771_198598296_198659753_198666156_RF OBD142_233 12 RGS6_14_72139099_72144564_72213251_72222544_FR OBD142_245 13 RUNX3_1_24920810_24923822_24973522_24976037_RF OBD142_253 14 ZFHX3_16_73147488_73153243_73182254_73184585_FF OBD142_325 15 MYOT_5_137829466_137834410_137882068_137884626_RR OBD142_341 16 AGT_1_230724515_230729957_230752057_230757333_RF OBD142_365 17 MYL1_2_210288997_210291732_210359762_210362293_FF OBD142_449 18 SRI_7_88199682_88203042_88229166_88237101_RF OBD142_509

TABLE 38.h Category Inner_primers High or PCR- Low PCR_Primer1 Primer2_ID PCR_Primer2 Responder 1 CACCTCAAAAGACAACCCCAGACCCA OBD142_027 CCCTCACTTTCCTTCTACTCTTCAAG Presence in strength high responder 2 GCTCCACATTTCCCAATCTAACCTGC OBD142_063 GTCAGAGTTGCCGATAGGTCTTGCTA Presence in strength high responder 3 AATCTCTGTCCCCAACTGTATCTGGC OBD142_091 ACATCTATCTTGCCCCTCACTCAGGT Presence in strength high responder 4 GAGTATTTACGATGGTCAGGTGCTGC OBD142_111 ATCCAAACACAGGACGAGAATAAAGC Presence in strength high responder 5 GACCTGTGGTTCTGACTGTCCAG OBD142_119 TATCGTCCAGGAGGCAAGGGTCC Presence in strength high responder 6 GCAACCTGGTCTCCTACCTGCTTCTA OBD142_147 GATGAGGTAACCAAAGTTCAGGGAGA Presence in strength high responder 7 TAGCAGACAATCAGAGGGTTTTGC OBD142_155 CTCTCTCCTCATCCTCCCTCCTAATA Presence in strength high responder 8 GCTGGTAGTTGGCTTTTGGGAAGAAC OBD142_159 GGGAGCCAGAAAGATAGCAATGCCTA Presence in strength high responder 9 TTCTCCCTCGGACGCTCATCCTC OBD142_191 GAGGAGGAGAAACTCAGAAGCCC Presence in strength high responder 10 CTGGAACTTGTTTAGGCACTGAAGCA OBD142_215 GCACAAGACCTCACATTCTGATGGGC Presence in strength high responder 11 GCAAAGGGCAGGTCATCATCATTCAA OBD142_235 CTCTCCTTTATCCCCTACCCTGCTCA Presence in strength high responder 12 CCCCGATGAATGTTACCCTGTCCC OBD142_247 CAGAGAAAGGGAGTTTGGAGGGC Presence in strength high responder 13 CTGAAATCCCATAGTGAGATGCCTTC OBD142_255 CCCCAAACTCCCAGACACATCAGAGA Presence in strength high responder 14 CCTGGATGTTCATTCCCACCTGG OBD142_327 AGAGGGAAAGGCAGGTCGTGAGC Presence in strength high responder 15 GCAGATTCCACAGGGCTTAC OBD142_343 GCTGGTCTCAAACTCCTGGG Presence in strength high responder 16 ACCCAACCCTGCTATACAATTCCA OBD142_367 GGGCATCMCCTCTTATTCAAGGT Presence in strength high responder 17 AGGAAATAGCCCAAATGCAACTGAA OBD142_451 ACAGTCAGTGATTGGCACAGAGTAA Presence in strength high responder 18 GAATGAAACTCTGAGGCCGG OBD142_511 CCCATTCGTCTCTCTGAGCTG Presence in strength high responder

TABLE 39.a Probe GeneLocus 1 THNSL2_2_88139809_88146295_88161717_88164554_FR THNSL2 E_Ctrl 2 IGF1R_15_98652565_98657862_98731539_98737034_RF IGF1R Str_Ctrl 3 DKK3_11_11956071_11968035_11984245_11993733_FR DKK3 Str_Trn 4 CBL_11_119249760_119252653_119294588_119299643_RF CBL E_Trn 5 EYA1_8_71216399_71218728_71261816_71267769_RR EYA1 Str_Trn 6 ACACB_12_109236052_109237242_109268078_109273323_RR ACACB E_Ctrl 7 PTPRC_1_198595771_198598296_198659753_198666156_RF PTPRC E_Ctrl

TABLE 40 Gene CV Only OBD142_513.515 SRI Shared OBD142_261.263 SMAD7 OBD142_313.315 WASL OBD142_021.023 B3GAT2 Strength Only OBD142_473.475 RB1 OBD142_389.391 MTFR1 OBD142_301.303 TLR2 OBD142_169.171 NFKB1 OBD142_173.175 NTRK2 OBD142_489.491 ITGAV OBD142_457.459 PPARA

No. Probe Loci 1 CBL_11_119249760_119252653_119294588_119299643_RF CBL Present in Endurance 2 DKK3_11_11956071_11968035_11984245_11993733_FR DKK3 Present in Strength 3 DKK3_11_11956071_11968035_12048403_12051930_FR DKK3 Present in Strength 4 FBXO32_8_123526212_123527874_123555254_123559065_FR FBXO32 Present in Endurance 5 KDM1A_1_23064655_23070269_23096951_23098159_FR KDM1A Present in Strength 6 EYA1_8_71216399_71218728_71261816_71267769_RR EYA1 Present in Strength 7 PCK1_20_57527297_57530814_57579772_57583521_RR PCK1 Present in Endurance 8 PIK3C3_18_42070009_42072187_42088671_42094691_FF PIK3C3 Present in Endurance 9 ALDH1A2_15_58053198_58062371_58157807_58162832_RR ALDH1A2 Present in Strength 10 CD36_7_80539507_80544315_80679651_80687690_FR CD36 Present in Strength 11 DKK3_11_11956071_11968035_12010923_12019458_FF DKK3 Present in Strength 12 IL1RAP_3_190489665_190498302_190560851_190563356_FR IL1RAP Present in Endurance 13 RUNX3_1_24920810_24923822_24973522_24976037_RF RUNX3 Present in Strength 14 PPARA_22_46101029_46102611_46241078_46244347_FR PPARA Present in Endurance 15 SLC25A13_7_96209525_96214524_96295606_96302029_FF SLC25A13 Present in Endurance 16 PCK1_20_57527297_57530814_57551578_57557205_RR PCK1 Present in Endurance 17 MYL1_2_210288997_210291732_210359762_210362293_FF MYL1 Present in Endurance 18 C1GALT1_7_7113076_7114831_7258228_7260668_FF C1GALT1 Present in Endurance 19 COL25A1_4_109024771_109031337_109090838_109104305_RR COL25A1 Present in Endurance 20 COL5A1_9_134738485_134741113_134811418_134816113_RR COL5A1 Present in Strength 21 DIAPH3_13_59818047_59823591_59854837_59860534_RR DIAPH3 Present in Endurance 22 FBLN2_3_13512352_13515076_13582406_13590343_RF FBLN2 Present in Endurance 23 GPC6_13_94121445_94133208_94296633_94304225_FF GPC6 Present in Strength 24 GSN_9_121177548_121180410_121268506_121274144_FR GSN Present in Endurance 25 GSN_9_121227501_121232628_121268506_121274144_FR GSN Present in Endurance 26 GSN_9_121239116_121243347_121268506_121274144_FR GSN Present in Endurance 27 LCK_1_32214585_32217213_32237144_32241139_RF LCK Present in Endurance 28 LMO4_1_87315524_87318670_87343110_87349940_FF LMO4 Present in Endurance 29 MAPK10_4_86572598_86581486_86617317_86621940_FF MAPK10 Present in Endurance 30 MBNL1_3_152229500_152234786_152281057_152285843_FR MBNL1 Present in Strength 31 NCAM1_11_113019160_113028536_113163748_113168132_FR NCAM1 Present in Endurance 32 PCK1_20_57527297_57530814_57570220_57572870_RR PCK1 Present in Endurance 33 PDK3_X_24441637_24447950_24480152_24481252_FR PDK3 Present in Endurance 34 PDK3_X_24441637_24447950_24490440_24491541_FR PDK3 Present in Endurance 35 PTPRC_1_198595771_198598296_198659753_198666156_RF PTPRC Present in Endurance 36 PTPRC_1_198659753_198666156_198721093_198724578_FF PTPRC Present in Endurance 37 RYR1_19_38410632_38413089_38495982_38499305_RR RYR1 Present in Strength 38 THNSL2_2_88139809_88146295_88161717_88164554_FR THNSL2 Present in Endurance 39 UACA_15_70715123_70719636_70780754_70784668_RF UACA Present in Endurance 40 ZEB1_10_31273317_31275631_31507470_31524442_FF ZEB1 Present in Endurance 41 ZFHX3_16_73147488_73153243_73182254_73184585_FF ZFHX3 Present in Strength 42 ADRB3_8_37962724_37965269_37987735_37989039_FR ADRB3 Present in Strength 43 AGT_1_230724515_230729957_230752057_230757333_RF AGT Present in Strength 44 HTR2A_13_46860092_46866824_46904346_46907815_RF HTR2A Present in Strength 45 SOS1_2_38982199_38993639_39061418_39066028_FF SOS1 Present in Strength 46 ACBD6_1_180431719_180434683_180541491_180549122_RR ACBD6 Present in Endurance 47 MYH1_17_10502067_10505465_10533547_10534931_RF MYH1 Present in Endurance 48 MYOD1_11_17685862_17689487_17729653_17733608_FR MYOD1 Present in Endurance 49 NECTIN3_3_111028574_111034204_111209684_111210764_FR NECTIN3 Present in Endurance 50 ACACB_12_109146008_109150083_109236052_109237242_RR ACACB Present in Endurance 51 ACACB_12_109236052_109237242_109268078_109273323_RR ACACB Present in Endurance 52 IGF1R_15_98652565_98657862_98731539_98737034_RF IGF1R Present in Strength 53 SOCS7_17_38347510_38348776_38360864_38363420_FR SOCS7 Present in Endurance 54 STXBP4_17_55035186_55042800_55117598_55123347_RR STXBP4 Present in Endurance 55 SVEP1_9_110397951_110405969_110503630_110509758_FF SVEP1 Present in Endurance 56 EMCN_4_100636305_100649860_100744427_100745788_RR EMCN Present in Endurance 57 ACACB_12_109146008_109150083_109185066_109187324_RR ACACB Present in Endurance 58 FOXO1_13_40524349_40526124_40688580_40690771_RR FOXO1 Present in Strength 59 FOXO3_6_108603215_108604436_108629992_108635481_FR FOXO3 Present in Endurance 60 FTO_16_53844989_53854574_54045378_54052319_RF FTO Present in Endurance 61 GPC6_13_94054831_94060621_94121445_94133208_RF GPC6 Present in Strength 62 PPP3CA_4_101055418_101067369_101247819_101259416_RR PPP3CA Present in Endurance 63 SMAD7_18_48917335_48920290_48969505_48974578_RF SMAD7 Present in Strength 64 SYK_9_90816328_90822228_90832284_90836084_RR SYK Present in Endurance 65 SYK_9_90816328_90822228_90872966_90875740_RR SYK Present in Endurance 66 TGFB2_1_218317687_218325587_218386401_218389011_FR TGFB2 Present in Endurance 67 TGFBR2_3_30566144_30567439_30694718_30698514_RR TGFBR2 Present in Strength 68 TLR2_4_153659613_153661830_153693586_153700349_RF TLR2 Present in Strength 69 SVEP1_9_110493529_110499578_110527410_110532406_FR SVEP1 Present in Strength 70 MTFR1_8_65658401_65661888_65780891_65782535_RF MTFR1 Present in Endurance 71 GSN_9_121182946_121189020_121323589_121328431_FF GSN Present in Strength 72 MUSK_9_110648469_110652659_110747866_110751903_FR MUSK Present in Strength 73 PPARA_22_46128634_46134707_46231440_46235124_FR PPARA Present in Strength 74 PPP1R9A_7_94903925_94908776_94951930_94967018_RF PPP1R9A Present in Endurance 75 PLCXD2_3_111633890_111638317_111672672_111677327_FR PLCXD2 Present in Endurance 76 SGCZ_8_14631157_14642508_14778176_14785491_FF SGCZ Present in Endurance 77 SRI_7_88199682_88203042_88229166_88237101_RF SRI Present in Endurance Table 41 shows markers identified in the human study, which are preferably used to type humans. 

1.-17. (canceled)
 18. A process for detecting a chromosome state which represents a subgroup in a population comprising determining whether a chromosome interaction relating to that chromosome state is present or absent within a defined region of the genome, wherein said subgroup relates to physical performance in an individual; and wherein the chromosome interaction either: (i) corresponds to any one of the chromosome interactions shown in any of Tables 3, 7, 8, 9, 25 and 30; and/or (ii) corresponds to any one of the chromosome interactions shown in any of Tables 13, 14, 18, 22, 23 and 24; and/or (iii) corresponds to any one of the chromosome interactions shown in Table 31 or
 32. 19. A process according to claim 18 wherein: the individual is a human and the subgroup is a human subgroup the individual is a horse and the subgroup is a horse subgroup, and wherein optionally: (i) the process is carried out to determine physical performance ability, and/or (ii) the process is carried out to detect responsiveness to a stimulus relating to physical performance, which is preferably physical training, and optionally strength or endurance training; and/or (iii) the process is carried out to select an individual suitable for a physical activity, which is preferably a sport; and/or (iv) the process is carried out to select a stimulus relating to physical performance to give to the individual, wherein said stimulus is a type of physical training.
 20. A process according to claim 18 wherein a specific combination of chromosome interactions are typed: (i) comprising all of the chromosome interactions represented in any of Tables 3, 7, 8, 9, 25 and 30 or any of Tables 13, 14, 18, 22, 23; and/or (ii) comprising at least 10%, 20%, 50%, or 80% of the chromosome interactions in any of Tables 3, 7, 8, 9, 25 and 30 or any of Tables 13, 14, 18, 22,
 23. 21. A process according to claim 18 wherein a specific combination of chromosome interactions are typed: (i) comprising all of the chromosome interactions represented in Table 31 or 32; and/or (ii) comprising at least 10%, 20%, 50%, or 80% of the chromosome interactions in Table 31 or
 32. 22. A process according to claim 18 in which the chromosome interactions are typed: in a sample from an individual, and/or by detecting the presence or absence of a DNA loop at the site of the chromosome interactions, and/or detecting the presence or absence of distal regions of a chromosome being brought together in a chromosome conformation, and/or by detecting the presence of a ligated nucleic acid which is generated during said typing and whose sequence comprises two regions each corresponding to the regions of the chromosome which come together in the chromosome interaction.
 23. A process according to claim 22 wherein said detecting of the ligated nucleic acid is by using either: (i) a probe that has at least 70% identity to any of the specific probe sequences mentioned in Table 24, 25, 30, 31 or 32; and/or (ii) by a primer pair which has at least 70% identity to any primer pair in Table 24, 25, 30, 31 or
 32. 24. A process according to claim 18, wherein the chromosome interaction is detected by a method comprising the steps of:— (i) cross-linking of chromosome regions which have come together in a chromosome interaction; (ii) subjecting said cross-linked regions to cleavage, optionally by restriction digestion cleavage with an enzyme; (iii) ligating said cross-linked cleaved DNA ends to form ligated nucleic acids; and (iv) detecting the presence or absence of a ligated nucleic acid corresponding to the chromosome interaction.
 25. A process according to claim 18: wherein at least 10 to 50 different chromosome interactions are typed; and/or which is: (i) carried out on a human or horse athlete; and/or (ii) carried out as part of a training regime, preferably after the start of the training regime; and/or (iii) carried out on a Thoroughbred horse, preferably a racing horse; or (iv) carried out on a human individual of who is less than 20 years old or is carried out on a horse that is less than 18 months old, and/or (v) which is carried out at multiple time points to assess physical performance characteristics at specific time points, wherein the process is optionally carried out at at least 3 time points, which are preferably at least 30 days apart from each other.
 26. A process according to claim 18: which is carried out to identify an individual that is suited to endurance training, and preferably the identified individual is then subject to endurance training, which optionally occurs on at least 100 days out of the next 365 days after the identification; or which is carried out to identify an individual that is suited to strength training, and preferably the identified individual is then subject to strength training, which optionally occurs on at least 100 days out of the next 365 days after the identification.
 27. A process according to claim 18 which is carried out to select the individual for racing.
 28. A process according to claim 18 wherein a specific combination of chromosome interactions are typed: (i) comprising all of the chromosome interactions represented in any of Tables 33, 34, 35, 36, 37, 38, 39, 40 or 41, or in any of FIG. 16, 17 or 18; and/or (ii) comprising at least 10%, 20%, 50%, or 80% of the chromosome interactions in any of Tables 33, 34, 35, 36, 37, 38, 39, 40 or 41, or in any of FIG. 16, 17 or
 18. 29. A process according to claim 18 which is carried out to identify or design an agent that affects physical performance, wherein said process is used to detect whether a candidate agent is able to cause a change to a chromosome state which is associated with a different physical performance state; wherein the chromosomal interaction is any specific interaction or combination of interactions defined in any preceding claim; and/or the change in chromosomal interaction is monitored using (i) a probe that has at least 70% identity to any of the specific probe sequences mentioned in Table 24, 25, 30, 31 or 32 and/or (ii) by a primer pair which has at least 70% identity to any primer pair in Table 24, 25, 30, 31 or
 32. 30. A process according to claim 18 which comprises selecting a target based on detection of chromosome interactions, and preferably screening for a modulator of the target to identify an agent which affects physical performance, wherein said target is optionally a protein.
 31. A process according to claim 18, wherein the typing or detecting comprises specific detection of the ligated product by quantitative PCR (qPCR) which uses primers capable of amplifying the ligated product and a probe which binds the ligation site during the PCR reaction, wherein said probe comprises sequence which is complementary to sequence from each of the chromosome regions that have come together in the chromosome interaction, wherein preferably said probe comprises: an oligonucleotide which specifically binds to said ligated product, and/or a fluorophore covalently attached to the 5′ end of the oligonucleotide, and/or a quencher covalently attached to the 3′ end of the oligonucleotide, and optionally said fluorophore is selected from HEX, Texas Red and FAM; and/or said probe comprises a nucleic acid sequence of length 10 to 40 nucleotide bases, preferably a length of 20 to 30 nucleotide bases.
 32. A process according to claim 18 which further comprises: producing a report on the physical performance characteristics of the individual based on the results of the process, or inputting the results of the process into a database, or assigning a specific fitness or training regime to the individual based on the results of the process, or designing a specific fitness or training regime for the individual based on the results of the process. 